A couple of suggestions.
If you are happy with your cabinet (and its games) the way it is, then stop updating it. Eventually you will find that the computer in your cabinet can no longer even handle the games you used to play as new Mame versions get slower and slower. You may find that games you like to play get broken in newer versions, you may lose your high scores or settings. I NEVER update any of my cabinets for all of these reasons.
If you must update (like you know, if you actually have a fast enough computer to handle the new releases and all the specialized analog controls needed to control them), then simply do this.
Split your rom files on your computer into two folders, one of which has the roms you keep on your cabinet, and the other one with the rest of them. Then you can keep it properly updated from there, and simply copy over that folder once you are done updating for each release.
Of course you COULD just read the release notes for changed roms, I mean you must be reading it anyway if you are downloading new versions with every release. And then download them all to a temp folder, copy that folder onto your cabinet, and then dump them into your main roms folder on your normal PC.