[2020] Steam thinks the game isn't installed. The files are still there, however.

I've not seen that before, with this or any other game. I assume running ck3.exe directly runs the game?

My instinct is to do a clean reinstall of Steam and game, would you be okay with that? I ask because I sense some reluctance on your part to do anything that dramatic!  

I don't see the need, but come back to us if you get any problem!