If I was you I’d be tempted to remove those configs with
“rm /opt/retropie/configs/all/retroarch-joypads/*.cfg”
Then run the controller registration for retroarch.
You can do this with
“sudo /home/pi/RetroPie-Setup/./retropie_setup.sh”
Then choose 3 – Setup
Then “Configure input devices for RetroArch”
That will then prompt you to press the buttons on your controller.
This video shows how to set the analogue stick to work as well.