Hi, I had the same predicament, so for example I'd set mine up with a fully scraped N64 list, however I'm no longer wanting to see them (mostly use an arcade stick rather than pad).
So, in the share\roms directory, I renamed the folder 'n64_' and created an empty folder called 'n64'.
Should I ever want to quickly see the N64 games, I will just rename the folder back to 'n64'. This way I don't need to re-transfer roms \ mess with scraping etc.
Hope that helps!