For some reason, whenever I switch my installation to and from Proton to test whether or not cloud saves are syncing correctly between Windows and Linux, I always end up with files I’ve deleted returning to the game.

After some fiddling around, I realized that this is because Steam Cloud only tracks file deletions that happen while the application is open and only propagates the deletion to other computers. Since Proton has its own save location, if I delete files on Proton then switch back to the Linux installation, the original files that were synced to Steam are still in my configuration folder on Linux. Since I’m still on the same computer, Steam thinks that the files are new instead of files that need to be deleted and syncs them.