diff --git a/annet/annlib/jsontools.py b/annet/annlib/jsontools.py
index c6596143..5849bdc6 100644
--- a/annet/annlib/jsontools.py
+++ b/annet/annlib/jsontools.py
@@ -28,7 +28,11 @@ def apply_json_fragment(
         try:
             new_value = pointer.get(new_fragment)
         except jsonpointer.JsonPointerException:
-            # no value found in new_fragment by the pointer, skip the ACL item
+            # no value found in new_fragment by the pointer,
+            # try to delete it from the new config
+            doc, part = pointer.to_last(full_new_config)
+            if isinstance(doc, dict) and isinstance(part, str):
+                doc.pop(part, None)
             continue
 
         _ensure_pointer_exists(full_new_config, pointer)