If you're talking about the Failed to create a game error, it shows up before I even seen you made a proton version.
Regarding the save file replaced by an empty one, I created the proton while the wine one was running (using same ports, so I expect it to fail, I just wanted to download the docker images). Then I turned off the Wine version, started Proton again, so it can download the game. At the end of the process, the save game was empty. I forgot to turn the server off before I added the save file (Oops). On restart, my save was replaced with an empty one. So this time, I turned it off properly, copy save file once again then started the server. It seems to work fine since.
To be clear, I don't need any assistance, things mostly works fine for me. I'm just sharing my experience in case it can help someone else to figure if something is “normal” or not ^^