Thank you for the help, @vinothkannans. I followed your instructions (took about 12 hours to execute) and the numbers have dropped somewhat:
22614 post uploads are missing.
19830 uploads are missing.
19821 of 19830 are old scheme uploads.
7339 of 535224 posts are affected.
As there are still missing uploads, I looked outside of the tombstone folder and found uploads/default on the live server is showing 22,885 empty directories (on the backup server it is 10 empty dirs). There is also a +10GB size difference on backup so I’m going to rsync uploads/default now from backup to live and then execute your instructions again.
Edit: rake posts:missing_uploads seems to be a CPU-bound single-threaded task that has been running for over 30 hours so I’ve rescaled the server onto a dedicated CPU instance temporarily. Images appear to have returned for the time being, albeit in the old scheme, so presumably some Discourse update had caused the original deletion in the first place.