When you run rebuilder there will be an option to remove files from the source folder or not, and whether to remove them if they exist in a defined rom folder I think.
To rebuild, get a dat from the version of mame you had before, add the mame 0.78 roms folder you just made as a source, and then you can run a missing file fix using the clrmamepro backup folder. All the roms that were not in 0.78 will either still be in your original folder or in the clrmamepro backup folder. (unless you completely disabled backups - unlikely)