diff --git a/surfsense_backend/app/connectors/composio_gmail_connector.py b/surfsense_backend/app/connectors/composio_gmail_connector.py
index 2a382f3b8..e675085db 100644
--- a/surfsense_backend/app/connectors/composio_gmail_connector.py
+++ b/surfsense_backend/app/connectors/composio_gmail_connector.py
@@ -463,7 +463,7 @@ async def _process_gmail_messages_phase2(
                 "connector_id": connector_id,
                 "source": "composio",
             }
-            safe_set_chunks(document, chunks)
+            await safe_set_chunks(session, document, chunks)
             document.updated_at = get_current_timestamp()
             document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/connectors/composio_google_calendar_connector.py b/surfsense_backend/app/connectors/composio_google_calendar_connector.py
index 63bade873..6344f9f38 100644
--- a/surfsense_backend/app/connectors/composio_google_calendar_connector.py
+++ b/surfsense_backend/app/connectors/composio_google_calendar_connector.py
@@ -477,7 +477,7 @@ async def index_composio_google_calendar(
                     "connector_id": connector_id,
                     "source": "composio",
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/connectors/composio_google_drive_connector.py b/surfsense_backend/app/connectors/composio_google_drive_connector.py
index c10edb7e9..30ce4a77b 100644
--- a/surfsense_backend/app/connectors/composio_google_drive_connector.py
+++ b/surfsense_backend/app/connectors/composio_google_drive_connector.py
@@ -1112,7 +1112,7 @@ async def _index_composio_drive_delta_sync(
                 "connector_id": connector_id,
                 "source": "composio",
             }
-            safe_set_chunks(document, chunks)
+            await safe_set_chunks(session, document, chunks)
             document.updated_at = get_current_timestamp()
             document.status = DocumentStatus.ready()
 
@@ -1520,7 +1520,7 @@ async def _index_composio_drive_full_scan(
                 "connector_id": connector_id,
                 "source": "composio",
             }
-            safe_set_chunks(document, chunks)
+            await safe_set_chunks(session, document, chunks)
             document.updated_at = get_current_timestamp()
             document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/services/linear/kb_sync_service.py b/surfsense_backend/app/services/linear/kb_sync_service.py
index 8d1bc47c7..4f97a3dd0 100644
--- a/surfsense_backend/app/services/linear/kb_sync_service.py
+++ b/surfsense_backend/app/services/linear/kb_sync_service.py
@@ -1,11 +1,10 @@
 import logging
 from datetime import datetime
 
-from sqlalchemy import delete
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from app.connectors.linear_connector import LinearConnector
-from app.db import Chunk, Document
+from app.db import Document
 from app.services.llm_service import get_user_long_context_llm
 from app.utils.document_converters import (
     create_document_chunks,
@@ -105,10 +104,6 @@ class LinearKBSyncService:
                 )
                 summary_embedding = embed_text(summary_content)
 
-            await self.db_session.execute(
-                delete(Chunk).where(Chunk.document_id == document.id)
-            )
-
             chunks = await create_document_chunks(issue_content)
 
             document.title = f"{issue_identifier}: {issue_title}"
@@ -131,7 +126,7 @@ class LinearKBSyncService:
                 "connector_id": connector_id,
             }
             flag_modified(document, "document_metadata")
-            safe_set_chunks(document, chunks)
+            await safe_set_chunks(self.db_session, document, chunks)
             document.updated_at = get_current_timestamp()
 
             await self.db_session.commit()
diff --git a/surfsense_backend/app/services/notion/kb_sync_service.py b/surfsense_backend/app/services/notion/kb_sync_service.py
index ce31e0d35..d6c64897f 100644
--- a/surfsense_backend/app/services/notion/kb_sync_service.py
+++ b/surfsense_backend/app/services/notion/kb_sync_service.py
@@ -1,10 +1,9 @@
 import logging
 from datetime import datetime
 
-from sqlalchemy import delete
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from app.db import Chunk, Document
+from app.db import Document
 from app.services.llm_service import get_user_long_context_llm
 from app.utils.document_converters import (
     create_document_chunks,
@@ -130,11 +129,6 @@ class NotionKBSyncService:
                 summary_content = f"Notion Page: {document.document_metadata.get('page_title')}\n\n{full_content}"
                 summary_embedding = embed_text(summary_content)
 
-            logger.debug(f"Deleting old chunks for document {document_id}")
-            await self.db_session.execute(
-                delete(Chunk).where(Chunk.document_id == document.id)
-            )
-
             logger.debug("Creating new chunks")
             chunks = await create_document_chunks(full_content)
             logger.debug(f"Created {len(chunks)} chunks")
@@ -147,7 +141,7 @@ class NotionKBSyncService:
                 **document.document_metadata,
                 "indexed_at": datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
             }
-            safe_set_chunks(document, chunks)
+            await safe_set_chunks(self.db_session, document, chunks)
             document.updated_at = get_current_timestamp()
 
             logger.debug("Committing changes to database")
diff --git a/surfsense_backend/app/tasks/connector_indexers/airtable_indexer.py b/surfsense_backend/app/tasks/connector_indexers/airtable_indexer.py
index 438a93815..6f020685a 100644
--- a/surfsense_backend/app/tasks/connector_indexers/airtable_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/airtable_indexer.py
@@ -432,7 +432,7 @@ async def index_airtable_records(
                         "table_name": item["table_name"],
                         "connector_id": connector_id,
                     }
-                    safe_set_chunks(document, chunks)
+                    await safe_set_chunks(session, document, chunks)
                     document.updated_at = get_current_timestamp()
                     document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/base.py b/surfsense_backend/app/tasks/connector_indexers/base.py
index 139aed1d3..b6ce2f2f9 100644
--- a/surfsense_backend/app/tasks/connector_indexers/base.py
+++ b/surfsense_backend/app/tasks/connector_indexers/base.py
@@ -28,45 +28,37 @@ def get_current_timestamp() -> datetime:
     return datetime.now(UTC)
 
 
-def safe_set_chunks(document: Document, chunks: list) -> None:
+async def safe_set_chunks(
+    session: "AsyncSession", document: Document, chunks: list
+) -> None:
     """
-    Safely assign chunks to a document without triggering lazy loading.
+    Delete old chunks and assign new ones to a document.
 
-    ALWAYS use this instead of `document.chunks = chunks` to avoid
-    SQLAlchemy async errors (MissingGreenlet / greenlet_spawn).
-
-    Why this is needed:
-    - Direct assignment `document.chunks = chunks` triggers SQLAlchemy to
-      load the OLD chunks first (for comparison/orphan detection)
-    - This lazy loading fails in async context with asyncpg driver
-    - set_committed_value bypasses this by setting the value directly
-
-    This function is safe regardless of how the document was loaded
-    (with or without selectinload).
+    This replaces direct ``document.chunks = chunks`` which triggers lazy
+    loading (and MissingGreenlet errors in async contexts).  It also
+    explicitly deletes pre-existing chunks so they don't accumulate across
+    repeated re-indexes — ``set_committed_value`` bypasses SQLAlchemy's
+    delete-orphan cascade.
 
     Args:
-        document: The Document object to update
-        chunks: List of Chunk objects to assign
-
-    Example:
-        # Instead of: document.chunks = chunks (DANGEROUS!)
-        safe_set_chunks(document, chunks)  # Always safe
+        session: The current async database session.
+        document: The Document object to update.
+        chunks: List of Chunk objects to assign.
     """
-    from sqlalchemy.orm import object_session
+    from sqlalchemy import delete
     from sqlalchemy.orm.attributes import set_committed_value
 
-    # Keep relationship assignment lazy-load-safe.
-    set_committed_value(document, "chunks", chunks)
+    from app.db import Chunk
 
-    # Ensure chunk rows are actually persisted.
-    # set_committed_value bypasses normal unit-of-work tracking, so we need to
-    # explicitly attach chunk objects to the current session.
-    session = object_session(document)
-    if session is not None:
-        if document.id is not None:
-            for chunk in chunks:
-                chunk.document_id = document.id
-        session.add_all(chunks)
+    if document.id is not None:
+        await session.execute(
+            delete(Chunk).where(Chunk.document_id == document.id)
+        )
+        for chunk in chunks:
+            chunk.document_id = document.id
+
+    set_committed_value(document, "chunks", chunks)
+    session.add_all(chunks)
 
 
 def parse_date_flexible(date_str: str) -> datetime:
diff --git a/surfsense_backend/app/tasks/connector_indexers/bookstack_indexer.py b/surfsense_backend/app/tasks/connector_indexers/bookstack_indexer.py
index bf3aaa35f..0660531b2 100644
--- a/surfsense_backend/app/tasks/connector_indexers/bookstack_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/bookstack_indexer.py
@@ -430,7 +430,7 @@ async def index_bookstack_pages(
                 document.content_hash = item["content_hash"]
                 document.embedding = summary_embedding
                 document.document_metadata = doc_metadata
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/clickup_indexer.py b/surfsense_backend/app/tasks/connector_indexers/clickup_indexer.py
index fd0233e87..af796ba3c 100644
--- a/surfsense_backend/app/tasks/connector_indexers/clickup_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/clickup_indexer.py
@@ -439,7 +439,7 @@ async def index_clickup_tasks(
                     "connector_id": connector_id,
                     "indexed_at": datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/confluence_indexer.py b/surfsense_backend/app/tasks/connector_indexers/confluence_indexer.py
index c28e82b8f..3495c59a4 100644
--- a/surfsense_backend/app/tasks/connector_indexers/confluence_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/confluence_indexer.py
@@ -413,7 +413,7 @@ async def index_confluence_pages(
                     "indexed_at": datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
                     "connector_id": connector_id,
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/discord_indexer.py b/surfsense_backend/app/tasks/connector_indexers/discord_indexer.py
index 0421352ff..e8e80a646 100644
--- a/surfsense_backend/app/tasks/connector_indexers/discord_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/discord_indexer.py
@@ -690,7 +690,7 @@ async def index_discord_messages(
                     "indexed_at": datetime.now(UTC).strftime("%Y-%m-%d %H:%M:%S"),
                     "connector_id": connector_id,
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/elasticsearch_indexer.py b/surfsense_backend/app/tasks/connector_indexers/elasticsearch_indexer.py
index 212afff39..f07c6c580 100644
--- a/surfsense_backend/app/tasks/connector_indexers/elasticsearch_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/elasticsearch_indexer.py
@@ -386,7 +386,7 @@ async def index_elasticsearch_documents(
                     document.content_hash = item["content_hash"]
                     document.unique_identifier_hash = item["unique_identifier_hash"]
                     document.document_metadata = metadata
-                    safe_set_chunks(document, chunks)
+                    await safe_set_chunks(session, document, chunks)
                     document.updated_at = get_current_timestamp()
                     document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/github_indexer.py b/surfsense_backend/app/tasks/connector_indexers/github_indexer.py
index fc6634024..61607dda3 100644
--- a/surfsense_backend/app/tasks/connector_indexers/github_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/github_indexer.py
@@ -415,7 +415,7 @@ async def index_github_repos(
                 document.content_hash = item["content_hash"]
                 document.embedding = summary_embedding
                 document.document_metadata = doc_metadata
-                safe_set_chunks(document, chunks_data)
+                await safe_set_chunks(session, document, chunks_data)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/google_calendar_indexer.py b/surfsense_backend/app/tasks/connector_indexers/google_calendar_indexer.py
index 1407d98dd..24e822060 100644
--- a/surfsense_backend/app/tasks/connector_indexers/google_calendar_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/google_calendar_indexer.py
@@ -528,7 +528,7 @@ async def index_google_calendar_events(
                     "indexed_at": datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
                     "connector_id": connector_id,
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/google_gmail_indexer.py b/surfsense_backend/app/tasks/connector_indexers/google_gmail_indexer.py
index 1a8b2b176..6e2408cbd 100644
--- a/surfsense_backend/app/tasks/connector_indexers/google_gmail_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/google_gmail_indexer.py
@@ -451,7 +451,7 @@ async def index_google_gmail_messages(
                     "date": item["date_str"],
                     "connector_id": connector_id,
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/jira_indexer.py b/surfsense_backend/app/tasks/connector_indexers/jira_indexer.py
index dec37428a..1765a592e 100644
--- a/surfsense_backend/app/tasks/connector_indexers/jira_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/jira_indexer.py
@@ -393,7 +393,7 @@ async def index_jira_issues(
                     "indexed_at": datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
                     "connector_id": connector_id,
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/linear_indexer.py b/surfsense_backend/app/tasks/connector_indexers/linear_indexer.py
index 1a2254c5b..bacafccc7 100644
--- a/surfsense_backend/app/tasks/connector_indexers/linear_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/linear_indexer.py
@@ -431,7 +431,7 @@ async def index_linear_issues(
                     "indexed_at": datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
                     "connector_id": connector_id,
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/luma_indexer.py b/surfsense_backend/app/tasks/connector_indexers/luma_indexer.py
index 2d86b09c1..83cf54f4e 100644
--- a/surfsense_backend/app/tasks/connector_indexers/luma_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/luma_indexer.py
@@ -488,7 +488,7 @@ async def index_luma_events(
                     "indexed_at": datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
                     "connector_id": connector_id,
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/notion_indexer.py b/surfsense_backend/app/tasks/connector_indexers/notion_indexer.py
index b0c49dea5..85daff94c 100644
--- a/surfsense_backend/app/tasks/connector_indexers/notion_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/notion_indexer.py
@@ -479,7 +479,7 @@ async def index_notion_pages(
                     "indexed_at": datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
                     "connector_id": connector_id,
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/obsidian_indexer.py b/surfsense_backend/app/tasks/connector_indexers/obsidian_indexer.py
index c0eef84d5..d53baa3b0 100644
--- a/surfsense_backend/app/tasks/connector_indexers/obsidian_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/obsidian_indexer.py
@@ -571,7 +571,7 @@ async def index_obsidian_vault(
                 document.content_hash = content_hash
                 document.embedding = embedding
                 document.document_metadata = document_metadata
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/slack_indexer.py b/surfsense_backend/app/tasks/connector_indexers/slack_indexer.py
index f83b171bc..1f2693844 100644
--- a/surfsense_backend/app/tasks/connector_indexers/slack_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/slack_indexer.py
@@ -564,7 +564,7 @@ async def index_slack_messages(
                     "indexed_at": datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
                     "connector_id": connector_id,
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/teams_indexer.py b/surfsense_backend/app/tasks/connector_indexers/teams_indexer.py
index ad34e8696..d04a98177 100644
--- a/surfsense_backend/app/tasks/connector_indexers/teams_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/teams_indexer.py
@@ -603,7 +603,7 @@ async def index_teams_messages(
                     "indexed_at": datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
                     "connector_id": connector_id,
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.updated_at = get_current_timestamp()
                 document.status = DocumentStatus.ready()
 
diff --git a/surfsense_backend/app/tasks/connector_indexers/webcrawler_indexer.py b/surfsense_backend/app/tasks/connector_indexers/webcrawler_indexer.py
index 94361cc27..4d2644420 100644
--- a/surfsense_backend/app/tasks/connector_indexers/webcrawler_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/webcrawler_indexer.py
@@ -410,7 +410,7 @@ async def index_crawled_urls(
                     "indexed_at": datetime.now().strftime("%Y-%m-%d %H:%M:%S"),
                     "connector_id": connector_id,
                 }
-                safe_set_chunks(document, chunks)
+                await safe_set_chunks(session, document, chunks)
                 document.status = DocumentStatus.ready()  # READY status
                 document.updated_at = get_current_timestamp()
 
diff --git a/surfsense_backend/app/tasks/document_processors/base.py b/surfsense_backend/app/tasks/document_processors/base.py
index 2edc48e91..580126d48 100644
--- a/surfsense_backend/app/tasks/document_processors/base.py
+++ b/surfsense_backend/app/tasks/document_processors/base.py
@@ -14,45 +14,37 @@ from app.db import Document
 md = MarkdownifyTransformer()
 
 
-def safe_set_chunks(document: Document, chunks: list) -> None:
+async def safe_set_chunks(
+    session: "AsyncSession", document: Document, chunks: list
+) -> None:
     """
-    Safely assign chunks to a document without triggering lazy loading.
+    Delete old chunks and assign new ones to a document.
 
-    ALWAYS use this instead of `document.chunks = chunks` to avoid
-    SQLAlchemy async errors (MissingGreenlet / greenlet_spawn).
-
-    Why this is needed:
-    - Direct assignment `document.chunks = chunks` triggers SQLAlchemy to
-      load the OLD chunks first (for comparison/orphan detection)
-    - This lazy loading fails in async context with asyncpg driver
-    - set_committed_value bypasses this by setting the value directly
-
-    This function is safe regardless of how the document was loaded
-    (with or without selectinload).
+    This replaces direct ``document.chunks = chunks`` which triggers lazy
+    loading (and MissingGreenlet errors in async contexts).  It also
+    explicitly deletes pre-existing chunks so they don't accumulate across
+    repeated re-indexes — ``set_committed_value`` bypasses SQLAlchemy's
+    delete-orphan cascade.
 
     Args:
-        document: The Document object to update
-        chunks: List of Chunk objects to assign
-
-    Example:
-        # Instead of: document.chunks = chunks (DANGEROUS!)
-        safe_set_chunks(document, chunks)  # Always safe
+        session: The current async database session.
+        document: The Document object to update.
+        chunks: List of Chunk objects to assign.
     """
-    from sqlalchemy.orm import object_session
+    from sqlalchemy import delete
     from sqlalchemy.orm.attributes import set_committed_value
 
-    # Keep relationship assignment lazy-load-safe.
-    set_committed_value(document, "chunks", chunks)
+    from app.db import Chunk
 
-    # Ensure chunk rows are actually persisted.
-    # set_committed_value bypasses normal unit-of-work tracking, so we need to
-    # explicitly attach chunk objects to the current session.
-    session = object_session(document)
-    if session is not None:
-        if document.id is not None:
-            for chunk in chunks:
-                chunk.document_id = document.id
-        session.add_all(chunks)
+    if document.id is not None:
+        await session.execute(
+            delete(Chunk).where(Chunk.document_id == document.id)
+        )
+        for chunk in chunks:
+            chunk.document_id = document.id
+
+    set_committed_value(document, "chunks", chunks)
+    session.add_all(chunks)
 
 
 def get_current_timestamp() -> datetime:
diff --git a/surfsense_backend/app/tasks/document_processors/circleback_processor.py b/surfsense_backend/app/tasks/document_processors/circleback_processor.py
index a86b64499..a6b9568b9 100644
--- a/surfsense_backend/app/tasks/document_processors/circleback_processor.py
+++ b/surfsense_backend/app/tasks/document_processors/circleback_processor.py
@@ -227,7 +227,7 @@ async def add_circleback_meeting_document(
         if summary_embedding is not None:
             document.embedding = summary_embedding
         document.document_metadata = document_metadata
-        safe_set_chunks(document, chunks)
+        await safe_set_chunks(session, document, chunks)
         document.source_markdown = markdown_content
         document.content_needs_reindexing = False
         document.updated_at = get_current_timestamp()
diff --git a/surfsense_backend/app/tasks/document_processors/extension_processor.py b/surfsense_backend/app/tasks/document_processors/extension_processor.py
index a6e482e15..7320ec9fa 100644
--- a/surfsense_backend/app/tasks/document_processors/extension_processor.py
+++ b/surfsense_backend/app/tasks/document_processors/extension_processor.py
@@ -21,6 +21,7 @@ from app.utils.document_converters import (
 from .base import (
     check_document_by_unique_identifier,
     get_current_timestamp,
+    safe_set_chunks,
 )
 
 
@@ -154,7 +155,7 @@ async def add_extension_received_document(
             existing_document.content_hash = content_hash
             existing_document.embedding = summary_embedding
             existing_document.document_metadata = content.metadata.model_dump()
-            existing_document.chunks = chunks
+            await safe_set_chunks(session, existing_document, chunks)
             existing_document.source_markdown = combined_document_string
             existing_document.updated_at = get_current_timestamp()
 
diff --git a/surfsense_backend/app/tasks/document_processors/file_processors.py b/surfsense_backend/app/tasks/document_processors/file_processors.py
index 5e97951bd..647435213 100644
--- a/surfsense_backend/app/tasks/document_processors/file_processors.py
+++ b/surfsense_backend/app/tasks/document_processors/file_processors.py
@@ -35,6 +35,7 @@ from .base import (
     check_document_by_unique_identifier,
     check_duplicate_document,
     get_current_timestamp,
+    safe_set_chunks,
 )
 from .markdown_processor import add_received_markdown_file_document
 
@@ -488,7 +489,7 @@ async def add_received_file_document_using_unstructured(
                 "FILE_NAME": file_name,
                 "ETL_SERVICE": "UNSTRUCTURED",
             }
-            existing_document.chunks = chunks
+            await safe_set_chunks(session, existing_document, chunks)
             existing_document.source_markdown = file_in_markdown
             existing_document.content_needs_reindexing = False
             existing_document.updated_at = get_current_timestamp()
@@ -622,7 +623,7 @@ async def add_received_file_document_using_llamacloud(
                 "FILE_NAME": file_name,
                 "ETL_SERVICE": "LLAMACLOUD",
             }
-            existing_document.chunks = chunks
+            await safe_set_chunks(session, existing_document, chunks)
             existing_document.source_markdown = file_in_markdown
             existing_document.content_needs_reindexing = False
             existing_document.updated_at = get_current_timestamp()
@@ -777,7 +778,7 @@ async def add_received_file_document_using_docling(
                 "FILE_NAME": file_name,
                 "ETL_SERVICE": "DOCLING",
             }
-            existing_document.chunks = chunks
+            await safe_set_chunks(session, existing_document, chunks)
             existing_document.source_markdown = file_in_markdown
             existing_document.content_needs_reindexing = False
             existing_document.updated_at = get_current_timestamp()
diff --git a/surfsense_backend/app/tasks/document_processors/markdown_processor.py b/surfsense_backend/app/tasks/document_processors/markdown_processor.py
index a8d20c062..d598bf9dd 100644
--- a/surfsense_backend/app/tasks/document_processors/markdown_processor.py
+++ b/surfsense_backend/app/tasks/document_processors/markdown_processor.py
@@ -21,6 +21,7 @@ from .base import (
     check_document_by_unique_identifier,
     check_duplicate_document,
     get_current_timestamp,
+    safe_set_chunks,
 )
 
 
@@ -258,7 +259,7 @@ async def add_received_markdown_file_document(
             existing_document.document_metadata = {
                 "FILE_NAME": file_name,
             }
-            existing_document.chunks = chunks
+            await safe_set_chunks(session, existing_document, chunks)
             existing_document.source_markdown = file_in_markdown
             existing_document.updated_at = get_current_timestamp()
             existing_document.status = DocumentStatus.ready()  # Mark as ready
diff --git a/surfsense_backend/app/tasks/document_processors/youtube_processor.py b/surfsense_backend/app/tasks/document_processors/youtube_processor.py
index 13b969fb6..0ed2e57d2 100644
--- a/surfsense_backend/app/tasks/document_processors/youtube_processor.py
+++ b/surfsense_backend/app/tasks/document_processors/youtube_processor.py
@@ -419,7 +419,7 @@ async def add_youtube_video_document(
             "author": video_data.get("author_name", "Unknown"),
             "thumbnail": video_data.get("thumbnail_url", ""),
         }
-        safe_set_chunks(document, chunks)
+        await safe_set_chunks(session, document, chunks)
         document.source_markdown = combined_document_string
         document.status = DocumentStatus.ready()  # READY status - fully processed
         document.updated_at = get_current_timestamp()
diff --git a/surfsense_backend/app/tasks/surfsense_docs_indexer.py b/surfsense_backend/app/tasks/surfsense_docs_indexer.py
index ca4a83de3..7d449c0ab 100644
--- a/surfsense_backend/app/tasks/surfsense_docs_indexer.py
+++ b/surfsense_backend/app/tasks/surfsense_docs_indexer.py
@@ -13,12 +13,32 @@ from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm import selectinload
 
+from sqlalchemy import delete as sa_delete
+from sqlalchemy.orm.attributes import set_committed_value
+
 from app.config import config
 from app.db import SurfsenseDocsChunk, SurfsenseDocsDocument, async_session_maker
 from app.utils.document_converters import embed_text
 
 logger = logging.getLogger(__name__)
 
+
+async def _safe_set_docs_chunks(
+    session: AsyncSession, document: SurfsenseDocsDocument, chunks: list
+) -> None:
+    """safe_set_chunks variant for the SurfsenseDocsDocument/Chunk models."""
+    if document.id is not None:
+        await session.execute(
+            sa_delete(SurfsenseDocsChunk).where(
+                SurfsenseDocsChunk.document_id == document.id
+            )
+        )
+        for chunk in chunks:
+            chunk.document_id = document.id
+
+    set_committed_value(document, "chunks", chunks)
+    session.add_all(chunks)
+
 # Path to docs relative to project root
 DOCS_DIR = (
     Path(__file__).resolve().parent.parent.parent.parent
@@ -156,7 +176,7 @@ async def index_surfsense_docs(session: AsyncSession) -> tuple[int, int, int, in
                 existing_doc.content = content
                 existing_doc.content_hash = content_hash
                 existing_doc.embedding = embed_text(content)
-                existing_doc.chunks = chunks
+                await _safe_set_docs_chunks(session, existing_doc, chunks)
                 existing_doc.updated_at = datetime.now(UTC)
 
                 updated += 1