Can your runls -la /opt/retropie/configs/all/retroarch-joypads/
and post the output ?
I would like to note that on another RPI 4 unit running 4.7.11 that the gamepad configurations do not save and when you exit a rom the controller is unresponsive.
This means the configuration of the gamepad is not saved in the EmulationStation's configuration file. Can you post the contents of $HOME/.emulationstation/es_input.cfg ?