Switching between docked mode and handheld mode the controllers (Xbox game controller/8BitDo controller) were not properly detected. Relaunching the game fixes the issue.

As many people, I was not able to import the save from Mask of Deception. At the time i didn't used ProtonDB and was not aware of the trick in the console. So i ended up using my Windows PC to import the save and create a Mask of Truth save. Once steam synced the saves I was able to start the game on the Steam Deck.

Later in the game there are some screens showing the advances in the maps/story telling that i noticed a performance hit. And just to make it crystal clear, It was not during game play/battles .