When get updated, ROMS (some) get changed.
REasons:
1. No good dump (got re-dumped for a new good one) (Maybe this is the case in your case) so the old one got removed.
2. ROMS gets added to a ROmSet (specially color proms)
3. HACKS REMOVE
4. ROMSET gets RENAME
5. I'm sure there is more for CHD's.
Anyway, my rule of thumb is, if MAME says its missing files, thats just it.

Thats why some keep older versions, just in case they need to run MAME in an oldier PC. Specially if they just want to run the classics.