I can't repeat that here. If I remove the files, ClrMamePro says they are missing in portman.
Using fixmissing adds them fine to the parent set (in full-merge mode).

Sounds like you already have the roms somewhere. Maybe in a not-merged cloneset (portman) in a different rompath. That could be the reason why it's not listed as missing. But you should see some 'wrong merged set' messages then (if 'sets' is enabled). Or they are in your parent set but with a wrong name and aren't listed as missing then.

..and of course use cmpro 3.02.2 ;)

Roman Scherzer
ClrMamePro