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 5cac13b1b..1d890c8d3 100644
--- a/surfsense_backend/app/tasks/connector_indexers/local_folder_indexer.py
+++ b/surfsense_backend/app/tasks/connector_indexers/local_folder_indexer.py
@@ -861,8 +861,12 @@ async def index_local_folder(
 
         root_fid = folder_mapping.get("")
         if root_fid:
+            from app.services.folder_service import get_folder_subtree_ids
+
+            subtree_ids = await get_folder_subtree_ids(session, root_fid)
             await _cleanup_empty_folders(
-                session, root_fid, search_space_id, existing_dirs, folder_mapping
+                session, root_fid, search_space_id, existing_dirs, folder_mapping,
+                subtree_ids=subtree_ids,
             )
 
         try:
diff --git a/surfsense_web/components/sources/FolderWatchDialog.tsx b/surfsense_web/components/sources/FolderWatchDialog.tsx
index bb3972a09..f6814bcfb 100644
--- a/surfsense_web/components/sources/FolderWatchDialog.tsx
+++ b/surfsense_web/components/sources/FolderWatchDialog.tsx
@@ -170,7 +170,7 @@ export function FolderWatchDialog({
 					<DialogDescription>Select a folder to sync and watch for changes.</DialogDescription>
 				</DialogHeader>
 
-				<div className="space-y-3 pt-2">
+				<div className="space-y-3 pt-2 min-h-[13rem]">
 					{selectedFolder ? (
 						<div className="flex items-center gap-2 py-1.5 pl-4 pr-2 rounded-md bg-slate-400/5 dark:bg-white/5 overflow-hidden">
 							<div className="min-w-0 flex-1 select-text">