You can rerun the MAME Full Set Import Wizard and uncheck more filters and it will add just those 'extra' games. Unless of course you uncheck 'ignore duplicates'. If you manually removed some games, they will get readded.
Conversely, if you run it again and check more of the filters (more that you had previously checked), it will not remove the games that fall under the newly checked coxes.
For this scenario, there's a plugin for that.
Arcade MAME ROMs are the exception for using "Scan for Added ROMs" in the Tools menu. That is, it doesn't (by design) work for them.