I had similar issue and I did a full re-install of Recalbox. I have all my games and configuration in an external WD Element HD connected to the RPI3 via USB. The good thing of this you don't need to mess about moving games and conf to the SD. All the configuration is inside the external HD. So, when reinstalling, you don't need to worry about the SD. Just reinstall and select the external HD as your preferred storage and all your roms and configuration will be there.