Up to v0.90 of MAMEWAH dealt with merged roms by using the -verifysets switch. Although I have removed this atm, it will be making an appearance again in I guess a few releases time...
Also, do you have a complete set? If so, then just use the 'DAT File Only' List Generation Method, and use a DAT file created with something like 'mame -listinfo > mame.dat'. This will show up all the roms, although if you do not have a complete set this may not be good.
Hopefully you haven't un-merged all your roms already!