diff --git a/changelog.d/11353.misc b/changelog.d/11353.misc
new file mode 100644
index 0000000000..fa96dae919
--- /dev/null
+++ b/changelog.d/11353.misc
@@ -0,0 +1 @@
+Fix an issue which prevented the 'remove deleted devices from `device_inbox` column' background process from running when updating from a recent Synapse version.
\ No newline at end of file
diff --git a/synapse/storage/schema/main/delta/65/05remove_deleted_devices_from_device_inbox.sql b/synapse/storage/schema/main/delta/65/06remove_deleted_devices_from_device_inbox.sql
similarity index 53%
rename from synapse/storage/schema/main/delta/65/05remove_deleted_devices_from_device_inbox.sql
rename to synapse/storage/schema/main/delta/65/06remove_deleted_devices_from_device_inbox.sql
index 076179123d..82f6408b36 100644
--- a/synapse/storage/schema/main/delta/65/05remove_deleted_devices_from_device_inbox.sql
+++ b/synapse/storage/schema/main/delta/65/06remove_deleted_devices_from_device_inbox.sql
@@ -18,5 +18,17 @@
 -- when a device was deleted using Synapse earlier than 1.47.0.
 -- This runs as background task, but may take a bit to finish.
 
+-- Remove any existing instances of this job running. It's OK to stop and restart this job,
+-- as it's just deleting entries from a table - no progress will be lost.
+--
+-- This is necessary due a similar migration running the job accidentally
+-- being included in schema version 64 during v1.47.0rc1,rc2. If a
+-- homeserver had updated from Synapse <=v1.45.0 (schema version <=64),
+-- then they would have started running this background update already.
+-- If that update was still running, then simply inserting it again would
+-- cause an SQL failure. So we effectively do an "upsert" here instead.
+
+DELETE FROM background_updates WHERE update_name = 'remove_deleted_devices_from_device_inbox';
+
 INSERT INTO background_updates (ordering, update_name, progress_json) VALUES
-  (6505, 'remove_deleted_devices_from_device_inbox', '{}');
+  (6506, 'remove_deleted_devices_from_device_inbox', '{}');