diff --git a/backend/open_webui/routers/files.py b/backend/open_webui/routers/files.py
index 7ca1c2e73f..f856d45785 100644
--- a/backend/open_webui/routers/files.py
+++ b/backend/open_webui/routers/files.py
@@ -50,6 +50,7 @@ from open_webui.storage.provider import Storage
 
 from open_webui.config import BYPASS_ADMIN_ACCESS_CONTROL, STORAGE_LOCAL_CACHE, STORAGE_PROVIDER, UPLOAD_DIR
 from open_webui.utils.auth import get_admin_user, get_verified_user
+from open_webui.utils.knowledge_collections import reindex_file_in_collection
 from open_webui.utils.misc import strict_match_mime_type
 from pydantic import BaseModel
 
@@ -577,14 +578,17 @@ async def update_file_data_content_by_id(
         knowledges = await Knowledges.get_knowledges_by_file_id(id, db=db)
         for knowledge in knowledges:
             try:
-                # Remove old embeddings for this file from the KB collection
-                await ASYNC_VECTOR_DB_CLIENT.delete(collection_name=knowledge.id, filter={'file_id': id})
-                # Re-add from the now-updated file-{file_id} collection
-                await process_file(
-                    request,
-                    ProcessFileForm(file_id=id, collection_name=knowledge.id),
+                # Rebuild first, then drop the stale vectors by their old ids.
+                # This preserves the previously indexed chunks if the rebuild fails.
+                await reindex_file_in_collection(
+                    request=request,
+                    file_id=id,
+                    collection_name=knowledge.id,
                     user=user,
                     db=db,
+                    process_file_form_factory=ProcessFileForm,
+                    process_file_func=process_file,
+                    vector_db_client=ASYNC_VECTOR_DB_CLIENT,
                 )
             except Exception as e:
                 log.warning(f'Failed to update knowledge {knowledge.id} after content change for file {id}: {e}')
diff --git a/backend/open_webui/test/util/test_knowledge_collections.py b/backend/open_webui/test/util/test_knowledge_collections.py
new file mode 100644
index 0000000000..ede7488df8
--- /dev/null
+++ b/backend/open_webui/test/util/test_knowledge_collections.py
@@ -0,0 +1,86 @@
+import asyncio
+from types import SimpleNamespace
+
+from open_webui.utils.knowledge_collections import reindex_file_in_collection
+
+
+def test_reindex_file_in_collection_deletes_old_ids_only_after_success():
+    calls = []
+
+    class DummyVectorDB:
+        async def query(self, collection_name, filter, limit=None):
+            calls.append(('query', collection_name, filter))
+            return SimpleNamespace(ids=[['old-1', 'old-2']])
+
+        async def delete(self, collection_name, ids=None, filter=None):
+            calls.append(('delete', collection_name, ids, filter))
+
+    async def fake_process_file(request, form, user, db):
+        calls.append(('process_file', form.file_id, form.collection_name))
+
+    class DummyProcessFileForm:
+        def __init__(self, file_id, collection_name=None):
+            self.file_id = file_id
+            self.collection_name = collection_name
+
+    asyncio.run(
+        reindex_file_in_collection(
+            request=object(),
+            file_id='file-1',
+            collection_name='kb-1',
+            user=object(),
+            db=None,
+            process_file_form_factory=DummyProcessFileForm,
+            process_file_func=fake_process_file,
+            vector_db_client=DummyVectorDB(),
+        )
+    )
+
+    assert calls == [
+        ('query', 'kb-1', {'file_id': 'file-1'}),
+        ('process_file', 'file-1', 'kb-1'),
+        ('delete', 'kb-1', ['old-1', 'old-2'], None),
+    ]
+
+
+def test_reindex_file_in_collection_preserves_old_ids_when_rebuild_fails():
+    calls = []
+
+    class DummyVectorDB:
+        async def query(self, collection_name, filter, limit=None):
+            calls.append(('query', collection_name, filter))
+            return SimpleNamespace(ids=[['old-1']])
+
+        async def delete(self, collection_name, ids=None, filter=None):
+            calls.append(('delete', collection_name, ids, filter))
+
+    async def fake_process_file(request, form, user, db):
+        calls.append(('process_file', form.file_id, form.collection_name))
+        raise RuntimeError('reindex failed')
+
+    class DummyProcessFileForm:
+        def __init__(self, file_id, collection_name=None):
+            self.file_id = file_id
+            self.collection_name = collection_name
+
+    try:
+        asyncio.run(
+            reindex_file_in_collection(
+                request=object(),
+                file_id='file-1',
+                collection_name='kb-1',
+                user=object(),
+                db=None,
+                process_file_form_factory=DummyProcessFileForm,
+                process_file_func=fake_process_file,
+                vector_db_client=DummyVectorDB(),
+            )
+        )
+        raise AssertionError('Expected reindex_file_in_collection to raise RuntimeError')
+    except RuntimeError as exc:
+        assert str(exc) == 'reindex failed'
+
+    assert calls == [
+        ('query', 'kb-1', {'file_id': 'file-1'}),
+        ('process_file', 'file-1', 'kb-1'),
+    ]
diff --git a/backend/open_webui/utils/knowledge_collections.py b/backend/open_webui/utils/knowledge_collections.py
new file mode 100644
index 0000000000..f2764386b1
--- /dev/null
+++ b/backend/open_webui/utils/knowledge_collections.py
@@ -0,0 +1,32 @@
+async def reindex_file_in_collection(
+    *,
+    request,
+    file_id: str,
+    collection_name: str,
+    user,
+    db,
+    process_file_form_factory,
+    process_file_func,
+    vector_db_client,
+) -> None:
+    result = await vector_db_client.query(
+        collection_name=collection_name,
+        filter={'file_id': file_id},
+    )
+
+    existing_ids = []
+    if result is not None and result.ids and result.ids[0]:
+        existing_ids = list(result.ids[0])
+
+    await process_file_func(
+        request,
+        process_file_form_factory(file_id=file_id, collection_name=collection_name),
+        user=user,
+        db=db,
+    )
+
+    if existing_ids:
+        await vector_db_client.delete(
+            collection_name=collection_name,
+            ids=existing_ids,
+        )