The rebuilding process keeps skipping files at random. I don't know why. In one it might skip 2 files and in another it might skip 16 files. It is the same source files. The conversion is from a merged set to a split set. I'm going to try to use the merger instead of the rebuilder though. However this should be fixed in the future. BTW, During the rebuild it had skipped 2 files that were required for a couple of sets. This was discovered during a scan of the resulting files. The source files were fine however.

EDIT:
My run in the merger ended even worse. Although no files were actually missing it did report that files were in the wrong set. Some files that were supposed to be in the clone set were actually in the parent set and vice-versa. In some cases the clone set wasn't even created.

I am using CLRMamePro 3.73.