@zing Couldn't post yesterday for some reason, I kept getting an error. But that idea did do the trick. Popped the second USB drive into the Pi and plugged it in, let Recalbox it do it's thing and build the folder structure then shut it down. Renamed the Recalbox folder on the SSD to something like recalbox_old, cut and pasted the new folders from the USB stick onto the SSD along side the old one. Cut and pasted everything important (bios files, roms, and saves) into the new folders and deleted the old ones with any old config files. Booted it up and everything was kosher again. I totally wasn't prepared to have to move everything off the SSD, just don't have the room anymore. Glad I didn't have to.