www.makemkv.com

I've seen this happen a few times now. Run makemkv.com on macOS 12.3, it creates the backup folder and the desktop displays the expected folder size (in GB). The first backup works fine, in fact they all seemingly feed Handbrake just fine.

However, after the first backup, the folder sizes become corrupt and disk utility detects a problem under First Aid. The folder size is displayed to be something like 9 MB, nothing like correct. Handbrake still seems to process the entire backup file correctly.

The backup folder size appears incorrect before Handbrake processes the backup, altho I suppose Handbrake could be doing something to the file system before MakeMkv runs a second time.

I'm not sure I understand your workflow. Are you using MakeMKV to make a decrypted backup of a blu-ray (or UHD)? Or are you using MakeMKV to make .mkv files directly from the disc? Or maybe using MakeMKV to make a backup first, then making .mkv files from the backup?

I use MakeMKV to make a backup of the disc on the ssd.
From the backup, Handbrake produces a .mp4.
The .mp4 is moved to the NAS.

I could try the Make .mkv option.