www.makemkv.com

Amazon retail disk.
Backup completed, but HandBrake want's nothing to do with the resulting directory.

Was able to reprocess with makeMKV after backup, but I did not need to do that previously.

At a guess, Dolby Atmos track. Handbrake does not support that for now, but you should gather up the HB logs and ask over on forums.handbrake.fr for more details.

If you process to MKV files with MakeMKV, you can exclude the Atmos track from the rip, which will make it usable in HB.

I ran into a similar problem. Handbrake "crashes" after a few minutes into the video.

I used FFMPEG and the resulting video "skips" at the same part where the Handbrake crashed.

As a way of testing if it is possible that the disc is somehow flawed, I cranked up the retry count to 99 and enabled "expert logging". No problems are reported on it and I still get the same crash on Handbrake and "skipping" on the FFMPEG output video.

I can only assume that this is some form of protection.

To be certain, I suggest getting the logs from your handbrake encode and head over to forum.handbrake.fr and see what they say. You WILL need the encode log, and there are instructions prominently posted on the forum explaining how to retrieve them.

For what it's worth, I ripped this BR with no problems just two nights ago. The resulting MKV file plays perfectly in WMP12. I have not tried re-encoding it, however.