diff --git a/modules/invenio-oaiserver/invenio_oaiserver/percolator.py b/modules/invenio-oaiserver/invenio_oaiserver/percolator.py
index fadb3585b5..93a17dc936 100644
--- a/modules/invenio-oaiserver/invenio_oaiserver/percolator.py
+++ b/modules/invenio-oaiserver/invenio_oaiserver/percolator.py
@@ -130,8 +130,9 @@ def get_record_sets(record):
             yield spec
 
     # get list of sets that match using percolator
-    index, doc_type = RecordIndexer().record_to_index(record)
     document = record.dumps()
+    document.pop('$schema', None)
+    index, doc_type = RecordIndexer().record_to_index(document)
 
     percolator_doc_type = _get_percolator_doc_type(index)
     _create_percolator_mapping(index, percolator_doc_type)
diff --git a/modules/weko-deposit/weko_deposit/api.py b/modules/weko-deposit/weko_deposit/api.py
index b7fc05ceb7..aba0729731 100644
--- a/modules/weko-deposit/weko_deposit/api.py
+++ b/modules/weko-deposit/weko_deposit/api.py
@@ -1595,21 +1595,20 @@ def delete_by_index_tree_id(cls, index_id: str, ignore_items: list = []):
         """
         if index_id:
             index_id = str(index_id)
-        obj_ids = next((cls.indexer.get_pid_by_es_scroll(index_id, only_latest_version=True)), [])
-        removed_records = []
+        obj_ids = next((cls.indexer.get_pid_by_es_scroll(index_id)), [])
         for obj_uuid in obj_ids:
             r = RecordMetadata.query.filter_by(id=obj_uuid).first()
             if r.json['recid'] in ignore_items:
                 continue
             r.json['path'].remove(index_id)
+            if index_id in r.json.get('_oai', {}).get('sets', []):
+                r.json['_oai']['sets'].remove(index_id)
             flag_modified(r, 'json')
             if r.json and not r.json['path']:
                 from weko_records_ui.utils import soft_delete
                 soft_delete(obj_uuid)
-                removed_records.append(r)
-        for r in removed_records:
             dep = WekoDeposit(r.json, r)
-            dep.indexer.update_es_data(dep, update_revision=False)
+            dep.indexer.update_es_data(dep, update_revision=False, update_oai=True)
 
     def update_pid_by_index_tree_id(self, path):
         """