@cyperghost ok I figured it out :)
it's a little bit of a bug but totally fixable.
ES uses both gamelist.xml found at /opt/retropie/configs/all/emulationstation/gamelists/"console"/ and /home/pi/RetroPie/roms/"console"/
so if there's no gamelist.xml in the console folder under roms, it will use the one found in configs. for some reason it doesn't remove entries, only adds them.
it will also not untag favorites if you DO have a gamelist.xml in your roms but DON'T have an entry in your gamelist.xml for the tagged favorite game.
Best word of advice: scrape like you've never scraped before lol