> Identical named but different hash-valued roms are in MAME since its beginning.
> If such a thing occurs within a parent/clone relationship, clrmamepro tells you
> while parsing the datfile/mame.exe.
>
> You go the option to either: split up parent/clone relationship for the sets in
> question, or force clrmamepro to work in split mode.

Hrm, I think for some reason ClrMame stopped doing this, as I had "Hide All" on - when you put on "Show Common" and select "Yes to All" for this does it remember you wanted to do that if you set it back to "Hide All"?

Why it broke so many of my sets is that it probably tried to merge them back into the same file, and didn't backup the file it replaced (or did so once, and then overwrote it on the next backup for identically named file).