Hello @nomadie, this reads like an issue with Steam managing wineprefixes rather than an issue with Proton itself, so I've transferred this issue report to the steam-for-linux issue tracker.
A couple details:
You've mixed memory and storage which made reading this issue report a bit harder to read than it needed to be.
Proton needs to setup a per-game wineprefix which Proton uses to approximate a Windows environment for each game. This is done locally rather than a separate download of Proton per game and can be about the size you've described. I would have expected that this would be stored in the same Steam library folder as the game, but the Steam client on the Steam Deck might be making a different choice for some reason. Why the internal SSD is being used instead of the external drive should be the focus of this issue report.
I suspect this is a duplicate of #7418.
If you go to a previously uninstalled game -> gear icon on the right -> Developer -> Delete Proton files, does this reclaim some of the free space that has gone missing? NOTE: If the game does not use cloud saves, then your save data might be lost.
It does reclaim some of the free space. That helps a bit. Sorry for the confusion as I did misword things. I will change that.
Yeah, I have no idea what is going on with it. I know it should put everything onto the External drive instead of the internal SSD.
I ended up giving up and just installed Windows 11.
Nothing extracted yet.
I don't think it's a bug but it's really, really bad.
So, I found I ended up switching to Windows 10 due to Proton eating up my internal storage
What happens is every time you download a new game on Steam it downloads Proton for that game which is like 250mb or so. If you got a 64gb version and don't have a larger internal drive you run out of room quickly.
So, I had a 6TB external drive pointed as my primary Steam Drive. I downloaded a bunch of games. I had 20gb left on my SteamOS drive before downloading games. I randomly got a low disk space error after downloading games. I was wondering what was going on since I have you know a 6TB drive. I found that Proton was eating up everything due to it downloading every single time I downloaded a game and it was downloaded to the SteamOS and not my 6TB drive.
You can uninstall the game but the Proton file stays on the SteamOS still.