I've created a support request, 07337909, but I just wanted to put this out here too.
We inherited a Veeam setup recently and they had a job configured with this:

They had a problem which caused the backups to all fail one night.
The next day I ran a "Quick Backup" of a selection of VMs from the job to make sure it would run ok.
After backing up the 3 VMs I'd selected Veeam started deleting all the backups and history from local and S3 storage for all the other VMs in the job.
12/07/2024 08:37:18 :: Backup '*** - *** is outdated and will be deleted
12/07/2024 08:51:12 :: Backup '*** - ***' is outdated and will be deleted
12/07/2024 08:52:47 :: Backup '*** - ***' is outdated and will be deleted
12/07/2024 08:54:42 :: Backup '*** - ***' is outdated and will be deleted
12/07/2024 08:54:42 :: Backup '*** - ***' is outdated and will be deleted
12/07/2024 09:06:32 :: Backup '*** - ***' is outdated and will be deleted
12/07/2024 09:09:37 :: Backup '*** - ***' is outdated and will be deleted
When I spotted this I stopped the job before it could delete the remaining 20 VMs from the backups.
This has got to be bug in Veeam's logic somewhere? Even if the tickbox to remove deleted items is ticked it shouldn't even consider going through the backups and deleting things when running a Quick Backup of a single (or in this case 3) VMs of a job containing 20+ VMs.
I've disabled the deletion of removed items for now but it's not going to get their backups back.
David