diff --git a/changelog.d/9503.bugfix b/changelog.d/9503.bugfix
new file mode 100644
index 000000000..086869138
--- /dev/null
+++ b/changelog.d/9503.bugfix
@@ -0,0 +1 @@
+Fix missing chain cover index due to a schema delta not being applied correctly. Only affected servers that ran development versions.
diff --git a/synapse/storage/databases/main/schema/delta/58/28rejected_events_metadata.sql b/synapse/storage/databases/main/schema/delta/59/09rejected_events_metadata.sql
similarity index 57%
rename from synapse/storage/databases/main/schema/delta/58/28rejected_events_metadata.sql
rename to synapse/storage/databases/main/schema/delta/59/09rejected_events_metadata.sql
index 9c9564628..cc9b267c7 100644
--- a/synapse/storage/databases/main/schema/delta/58/28rejected_events_metadata.sql
+++ b/synapse/storage/databases/main/schema/delta/59/09rejected_events_metadata.sql
@@ -13,5 +13,14 @@
  * limitations under the License.
  */
 
+-- This originally was in 58/, but landed after 59/ was created, and so some
+-- servers running develop didn't run this delta. Running it again should be
+-- safe.
+--
+-- We first delete any in progress `rejected_events_metadata` background update,
+-- to ensure that we don't conflict when trying to insert the new one. (We could
+-- alternatively do an ON CONFLICT DO NOTHING, but that syntax isn't supported
+-- by older SQLite versions. Plus, this should be a rare case).
+DELETE FROM background_updates WHERE update_name = 'rejected_events_metadata';
 INSERT INTO background_updates (ordering, update_name, progress_json) VALUES
   (5828, 'rejected_events_metadata', '{}');