Here are some database queries to get you started. This query will find submission files that are supposed to be attached to notes, but are not because the notes are gone
SELECT * FROM submission_files WHERE assoc_type = '520' AND assoc_id NOT IN (SELECT note_id from notes)
If you get any records back from that, you can use the file_id of those records to clean out corresponding records in the submission_file_settings, submission_file_revisions, and files tables.
For the latter two, there is a foreign key constraint on the file_id (this is new in OJS 3.3) and so if you are deleting records via PHPMyAdmin you’ll need to uncheck the box that says “Enable foreign key checks” or the command will fail. The files table records for those orphaned files will contain the path to the file on disk, in case you want to send them to the editor since once you delete the records from the database they’ll no longer be accessible on the workflow.
Please make a backup of your database before running these commands since there is no way to undo this except via a restore.
Best,
Jason