1)Profiler, create new profile based on latest mame binary. load the profile, answer all prompts with ok to all, yes to all.
2)Settings, add a new rompath...which in your case should be an empty folder.
3) rebuilder, set the just added rompath as destination. depending on the used archive type you can disable recompression.
Now Dragn drop the folder(s) with your advmame roms into the rebuilder.
anything valid will be recreated in the destination, your new rompath.
4) after that, you can use the scanner to see what is still missing.
find the missing files and simply dragn drop them in the scanner which acts like using the rebuilder to add files...repeat this until you're done.
thats one way, another one could be:.if advmame and mame are rather identical you might be able to set the path where your advmame roms are stored as rompath and simply use the scanner to fix the problems...so basically 1), 2), 4)