@nixzero said in How to save controller configurations to IMG backup?:

One thing worth mentioniing is that whenever I would configure the gamepad in ES (back when it was working), the gamepad would always have some random number. "GAMEPAD 20" or "GAMEPAD 5". I thought it was strange that it didn't always say 1 or 2 since I only have 2 controllers connected, and if it's creating profiles it appears to be numbering them randomly.

The numbering is not random and it starts from 1, but if the controller disconnects and re-connects the number is increased. This means that the controller(s) are disconnecting from your Pi for some reason and this might explain why they're not working correctly.

The fact that RetroArch finds the configuration (the messages "Honey Bee Quasi Con controller is configured in port 1/2" indicates that) means the configuration files are ok.

You should check by running dmesg -w from a SSH session, while the emulators are loading/runing, if the gamepads are disconnecting from the USB port when you start the emulator and/or when working in EmulationStation.