diff --git a/surfsense_backend/app/tasks/connector_indexers/local_folder_indexer.py b/surfsense_backend/app/tasks/connector_indexers/local_folder_indexer.py
index 591914625..93c6649a2 100644
--- a/surfsense_backend/app/tasks/connector_indexers/local_folder_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/local_folder_indexer.py
@@ -610,12 +610,25 @@ async def index_local_folder(
         # ================================================================
         # PHASE 1.5: Delete documents no longer on disk
         # ================================================================
+        # Collect ALL folder IDs under this root (including folders that no
+        # longer exist on disk but still have rows in the DB) so we catch
+        # documents in deleted directories too.
+        all_root_folder_ids = set(folder_mapping.values())
+        all_db_folders = (
+            await session.execute(
+                select(Folder.id).where(
+                    Folder.search_space_id == search_space_id,
+                )
+            )
+        ).scalars().all()
+        all_root_folder_ids.update(all_db_folders)
+
         all_folder_docs = (
             await session.execute(
                 select(Document).where(
                     Document.document_type == DocumentType.LOCAL_FOLDER_FILE,
                     Document.search_space_id == search_space_id,
-                    Document.folder_id.in_(list(folder_mapping.values())),
+                    Document.folder_id.in_(list(all_root_folder_ids)),
                 )
             )
         ).scalars().all()
diff --git a/surfsense_backend/tests/integration/indexing_pipeline/test_local_folder_pipeline.py b/surfsense_backend/tests/integration/indexing_pipeline/test_local_folder_pipeline.py
index e46d59a67..34efad789 100644
--- a/surfsense_backend/tests/integration/indexing_pipeline/test_local_folder_pipeline.py
+++ b/surfsense_backend/tests/integration/indexing_pipeline/test_local_folder_pipeline.py
@@ -485,8 +485,8 @@ class TestFolderMirroring:
             )
         ).scalars().all()
 
-        today_doc = next(d for d in docs if d.title == "today")
-        root_doc = next(d for d in docs if d.title == "root")
+        today_doc = next(d for d in docs if d.title == "today.md")
+        root_doc = next(d for d in docs if d.title == "root.md")
 
         daily_folder = (
             await db_session.execute(