Weird. Each compatibility game should be running on their own proton prefix, each prefix is independent and changes to one game environment should never affect other games. Soldier configures it all automatically. I’ve never had to clear “downloads cache?” I wouldn’t even know where that is. How did you debug the issue, did you try protontricks? It makes directX and other common tinkering options simple.
Also, 40 minutes to compile shaders, even if it’s just once on first run, sounds sus. I’ve never had a game take longer that maybe 5. Maybe there’s something else in your system interfering? Do you happen to have Nvidia, by chance?