I had the same bug after 1.2 patch. After two days of my investigation i manage to fix it.
U need to delete(or move) folder "Pillars of Eternity II" from "\Users\Username\AppData\LocalLow\Obsidian Entertainment". I have no idea where it can be on linux but i hope that you will find it.
After this, game should create new folder on startup. I dont know why, but now it's working fine for me.