Ok, please be patient with my questions, as I'm not sure entirely of how CLRMamePro is handling rom sets, and I'd like more experienced advice!

What I was after was simply a rename for all ROMS which were out of date, and a pointer towards which ROMS in my folder were no longer working and needed updating.

Firstly, I set downloaded the latest version, and set up a profile with Mame32.exe (85.3_Binary), pointing it to the ROMS and SAMPLES folders. I then performed a scan, with all options except "Missing" checked for a scan, everything else set as default. It listed a number of errors, which is irrelevant for now... I then ran it again, checking "Fix" for Case, Unneeded, Name and Size. It removed all but one error, which is in a BIOS, a missing file.

Now... When I started MAME before running CLRMamePRO, it showed a figure of 796 Titles Available, from a folder with 777 non-BIOS roms: It now shows only 754 Titles available: There's a number of clones that seem to perhaps have been merged into others (despite it being left on the default of Split Sets, as I had a few clone zips in there too... 2 Grobda clones have vanished, for instance) and some parent roms that don't appear at all... Skykid being one, although Skykid Deluxe is still visible. More worryingly, although the Skykid ROM exists still in the ROM folder, there is no copy of it in CLR's Backup.

So to the questions: What exactly has CLRMamePRO done with these fixes? Because as far as I can see, it's broken rather than fixed an awful lot of files which did work under the same MAME Build.
Is it possible to roll back the changes and return the roms to how they were before being fixed? I don't see anything in the documentation which indicates it can be done via CLR, but copying the files back to the ROM folder obviously won't work, as there are a few which won't be written over, like Skykidd as mentioned above.
And finally: is there anyway to get MAME to do a print of the files it see's under Available? As that would make a manual audit as compared to a list of the zip files in the ROMs folder, much, much easier...

Sorry to be such a noob, but compared to standard system emulation, I'm in way over my head with Multiple Arcade Machines!