On Linux I have 3 directories:
Pillars of Eternity II
PillarsofEternityII
PillarsOfEternityII (/SavedGames)
I believe this is what is happening, but I may be wrong on some details. On Linux system game looks into PillarsOfEternityII/SavedGames to save and load games. When you close your game on Linux, your saved files are supposed to be synced into cloud, but instead this happens: Pillars of Eternity II => Cloud When you run game again, your steam cloud saves are supposed to be synced back to your system but instead of putting them into PillarsOfEternityII/SavedGames this is what happens: Cloud => Pillars of Eternity II Cloud => PillarsofEternityII The wierd thing is that "Pillars of Eternity II" and PillarsofEternityII contain not exactly the same files on my system. It seems, that the former one contain the latest of my saved games while the latter lags behind. By the way, on my Windows those two directories are also present. While on Windows game correctly uses "Pillars of Eternity II" directory to read and sync saves, it seems to ignore the other directory. Workaround here on Linux is to symlink PillarsOfEternityII/SavedGames to "Pillars of Eternity II". You will still have three saved games directories, but syncing will work as expected.