This is if you controller is working fine in the Steam menu once you wake your Steam Deck but unresponsive in the game you was playing.

Press the Steam button, click on the game up the top and go into “Controller Settings”, you should see up the very top of the screen, your controller name and “Steam Deck”, just under that to the right, you will see “Reorder Controls”. Select that and change your controller to “2”, so “Steam Deck” Controller is now “1”.

This should now let the controller work in game again. I have seen no issue so far playing as controller “2” for this fix. And it sure beats closing the game in case you lose data.

From Reddit but a very useful tidbit