Not sure if this is what you mean... but I am using this great little GameList editor: https://forum.recalbox.com/topic/9265/soft-gamelist-editor

You can activate the "god-mode" and then you'll be able to select and remove roms, as well as the entries from the gamelist.xml.
You just have to give the path of the roms folder.

Buenas

Yo he hecho exactamente lo mismo hace una semana con el romset FBA v0.2.97.42.
He utilizado un software que se llama simple arcade multifilter. Para ello seguí este tutorial
Si necesitas ayuda me dices, un saludo