In /etc/emulationstation or /home/pi/.emulationstation there’s a file called es_input.cfg I believe. You can delete the old configs on there so that when it reboots it will ask you to configure your controller again (leave the first line that calls the input configuration.sh as that calls the scripts that configure retroarch configs. ) do you not have a keyboard to work with?
FINALLY. I was able to get ES to start over by removing the es_input.cfg file that was in the pi folder.
Now I need to configure each system it seems. SNES didn’t work.