Nope on the first, the backup is not in the rompath. The rompath in this case was "E:\Microsoft\XBox\Redump (Discs)" which is a SMB share on a TrueNAS NAS. The backup is locate at "D:\Emu\Tools\clrmamepro\backup" which is an internal hard drive on my local computer and is the same for all DATs. I do have remove source files selected, as well as use backup.
So, I had a window open (XYplorer instead of explorer) in the Xbox subdirectory of the backup directory, and I'm 95% sure inside the _unknown folder. I had a batch running of 200 no-intro DATs. It was on the Xbox DAT when I noticed it was backing up a lot of files that I didn't need, specifically in that set. I used another open XYplorer window to delete the unwanted files from the ROM directory that were left, except for the one it was currently processing. After it finished copying that one file to backup, it presented an error (sorry, didn't capture it) that said something to the effect of no files will be changed (?). It then wrote the remaining files to the output log indicating it was not processing them. At that point it moved on to the next DAT, while at the same time I saw all the files disappear from the Xbox backup directory in the window I had open. There were at least a dozen files, probably more, that it had backed up before my foolish deletion.
That's essentially it. Hopefully that's a little more clear.