First, make sure your PC and your Steam deck are running the same version of the game. Different versions cause incompatible saves.

Try the following to fix it:
Set the game to run under Proton Experimental on the Deck. This forces it to run the Windows version of the game, not the Linux version which has saves in a different location. (At the game page in your library, click the gear icon, Properties, and Compatibility. Click the check box to "Force the use..." and select Proton Experimental). Once that is done, cloud saves should work fine between PC and the Deck.

Lastly, please post whether or not this works for you, as it could also help somebody else with the same problem.

I'll first address the input issue. I had to manually change the layout for the game to a mouse only layout (Valve has it set to a joystick layout by default which has no mouse input). It used to be like this, but for some reason the default has changed there (which makes it impossible to enter the game). I will try your advice for the save now.

I tried your solution for the proton experimental and it seems like it doesn't even share the same save as windows (showing 0% where my windows is 2%). Its ok, I'll just stick to playing it on the deck.

Thanks for reporting back. That advice has worked before for Deck some problems on other games. Apparently they've updated the system and "broke it" again.