diff --git a/backend/danswer/datastores/datastore_utils.py b/backend/danswer/datastores/datastore_utils.py
index 6121ad899..9359562ab 100644
--- a/backend/danswer/datastores/datastore_utils.py
+++ b/backend/danswer/datastores/datastore_utils.py
@@ -8,10 +8,7 @@ from pydantic import BaseModel
 from danswer.chunking.models import EmbeddedIndexChunk
 from danswer.chunking.models import IndexChunk
 from danswer.chunking.models import InferenceChunk
-from danswer.configs.constants import ALLOWED_GROUPS
-from danswer.configs.constants import ALLOWED_USERS
 from danswer.configs.constants import PUBLIC_DOC_PAT
-from danswer.connectors.models import Document
 from danswer.connectors.models import IndexAttemptMetadata
 
 
@@ -55,7 +52,7 @@ T = TypeVar("T")
 
 
 def _add_if_not_exists(l: list[T], item: T) -> list[T]:
-    if item not in l:
+    if item in l:
         return l
     return l + [item]
 
diff --git a/backend/danswer/datastores/indexing_pipeline.py b/backend/danswer/datastores/indexing_pipeline.py
index d0bb79d83..c3a0be0d9 100644
--- a/backend/danswer/datastores/indexing_pipeline.py
+++ b/backend/danswer/datastores/indexing_pipeline.py
@@ -58,6 +58,9 @@ def _get_net_new_documents(
     net_new_documents = 0
     seen_documents: set[str] = set()
     for insertion_record in insertion_records:
+        if insertion_record.already_existed:
+            continue
+
         if insertion_record.document_id not in seen_documents:
             net_new_documents += 1
             seen_documents.add(insertion_record.document_id)
@@ -81,6 +84,7 @@ def _indexing_pipeline(
     keyword_store_insertion_records = keyword_index.index(
         chunks=chunks, index_attempt_metadata=index_attempt_metadata
     )
+    logger.debug(f"Keyword store insertion records: {keyword_store_insertion_records}")
     _upsert_insertion_records(
         insertion_records=keyword_store_insertion_records,
         index_attempt_metadata=index_attempt_metadata,
@@ -94,6 +98,7 @@ def _indexing_pipeline(
     vector_store_insertion_records = vector_index.index(
         chunks=chunks_with_embeddings, index_attempt_metadata=index_attempt_metadata
     )
+    logger.debug(f"Vector store insertion records: {keyword_store_insertion_records}")
     _upsert_insertion_records(
         insertion_records=vector_store_insertion_records,
         index_attempt_metadata=index_attempt_metadata,
diff --git a/backend/danswer/datastores/qdrant/indexing.py b/backend/danswer/datastores/qdrant/indexing.py
index 5e60d5650..5d0f445e1 100644
--- a/backend/danswer/datastores/qdrant/indexing.py
+++ b/backend/danswer/datastores/qdrant/indexing.py
@@ -111,6 +111,8 @@ def index_qdrant_chunks(
     cross_connector_document_metadata_map: dict[
         str, CrossConnectorDocumentMetadata
     ] = {}
+    # document ids of documents that existed BEFORE this indexing
+    already_existing_documents: set[str] = set()
     for chunk in chunks:
         document = chunk.source_document
         (
@@ -130,6 +132,7 @@ def index_qdrant_chunks(
         if should_delete_doc:
             # Processing the first chunk of the doc and the doc exists
             delete_qdrant_doc_chunks(document.id, collection, q_client)
+            already_existing_documents.add(document.id)
 
         for minichunk_ind, embedding in enumerate(chunk.embeddings):
             qdrant_id = str(get_uuid_from_chunk(chunk, minichunk_ind))
@@ -137,7 +140,7 @@ def index_qdrant_chunks(
                 ChunkInsertionRecord(
                     document_id=document.id,
                     store_id=qdrant_id,
-                    already_existed=should_delete_doc,
+                    already_existed=document.id in already_existing_documents,
                 )
             )
             point_structs.append(
diff --git a/backend/danswer/datastores/typesense/store.py b/backend/danswer/datastores/typesense/store.py
index d47492e65..abd87d3df 100644
--- a/backend/danswer/datastores/typesense/store.py
+++ b/backend/danswer/datastores/typesense/store.py
@@ -128,6 +128,8 @@ def index_typesense_chunks(
     cross_connector_document_metadata_map: dict[
         str, CrossConnectorDocumentMetadata
     ] = {}
+    # document ids of documents that existed BEFORE this indexing
+    already_existing_documents: set[str] = set()
     for chunk in chunks:
         document = chunk.source_document
         (
@@ -147,13 +149,14 @@ def index_typesense_chunks(
         if should_delete_doc:
             # Processing the first chunk of the doc and the doc exists
             delete_typesense_doc_chunks(document.id, collection, ts_client)
+            already_existing_documents.add(document.id)
 
         typesense_id = str(get_uuid_from_chunk(chunk))
         insertion_records.append(
             ChunkInsertionRecord(
                 document_id=document.id,
                 store_id=typesense_id,
-                already_existed=should_delete_doc,
+                already_existed=document.id in already_existing_documents,
             )
         )
         new_documents.append(