Tangentially related: I’ve had this exact problem with quite a few games. Most recently, Subnautica: Below Zero. I often pause a game, go take care of a chore or something, then come back to having no controller input. Only recourse seems to be to exit the game and start it back up again. Using an 8bitdo Ultimate (non bluetooth) controller at the moment, Steam Deck connected to the official dock.
Anyone else have this issue? Any remedies you’re aware of?
I’ll keep that in mind, thanks.