diff --git a/misc/migration_tools/rebuild_zebra.pl b/misc/migration_tools/rebuild_zebra.pl
index db5ee8809f..0dbeb9c99f 100755
--- a/misc/migration_tools/rebuild_zebra.pl
+++ b/misc/migration_tools/rebuild_zebra.pl
@@ -241,6 +241,7 @@ sub index_records {
             }
             if ($num_records_exported){
                 do_indexing($record_type, 'update', "$directory/upd_$record_type", $reset, $noshadow, $record_fmt, $zebraidx_log_opt);
+                mark_zebraqueue_batch_done($soft_deleted_entries);
                 mark_zebraqueue_batch_done($updated_entries);
             }
         } else {