OK, first things first, Launchbox does not officially support software lists, so there is no guidance for that as its simply not something we support. However there is a plugin in the downloads section that should help, but obviously the devs and moderators cannot provide support for a third party plugin, so use at your own risk and always backup your data first.
As for the standard Arcade games, just run the fullset importer again, pointed at your new MAME.exe and your new roms folder, and uncheck all the media downloads.