Please add some info about your setup, as requested in https://retropie.org.uk/forum/topic/3/read-this-first.

Mapping are usually created based on the controller/gamepad name, so even if the gamepad disconnects and then re-connects the configuration would still work. I'm not familiar with Arcade1Up inputs - are they using an USB encoder for both players or each player is a separate controller ?

Connect a keyboard and exit EmulationStation by pressing F4. From the command line, run

cd RetroPie-Setup sudo ./retropie_setup.sh

the reset the inputs from:

Configuration/Tools ➤ emulationstation ➤ Clear / Reset EmulationStation Input Configuration

You can then start back EmulationStation by typing emulationstation and you should get prompted to configure your gamepad again.

@mitu
Yeah, still no luck. So strange, as I had been able to use my gamepads in Xinput mode for at least a couple years from maybe 2019 onward till I updated my whole RetroPie OS and packages just a couple weeks ago. However, in going through the comments in github for xpad, it does seem like others are having issues with connecting their wired controllers through Xinput mode. Either way, thanks for your help up to this point and I'll keep digging around.

@Mailo

Nice to hear that you have found it.