This was a baseline MAME change. A large number of clones had expanded filenames to allow better identification and expanded detail in the setname. The previous 8 letter restriction was becoming very difficult to handle. Most people didn't notice because their auditing tool did the renaming for them.
Your best bet is to change them as you need them or find some sort of auditing tool to assist you.
Personally, I think it'd be nice if there were some sort of aliasing system such that you can define your own subtitute ROM names, and thus continue using the old names, but that'd be a bit much to ask.