Things like FileZilla, Midnight Commander, WinSCP, etc should work fine to do that (It shouldn't matter for doing this but you may want to have emulationstation closed), but honestly, for ease of access, i'd just enable the samba sharing feature and access the roms folder from the file explorer.
Depending on how much you've scraped and whether you'd want to do it again, you could try deleting the gamelist.xml also.