I have this problem with Skyrim and Fallout 4 if I use an external controller (either USB or Bluetooth) when docked. If the controller gets disconnected or I touch any of the Deck’s own controls when playing, the game will just completely stop listening to the external controller and will only work if I use the Deck’s controls. Restarting the game does fix it but it’s pretty annoying, and eg. toggling steam input off and on doesn’t do anything and the controller order is correct.