This is a very, very weird bug and after trying to fix it for a few days i found a way to fix it for my system:The way i resolved it was to delete everytthing in the appdata directory [C:\Users\User\AppData\Local\Temp\Obsidian Entertainment and C:\Users\User\AppData\LocalLow\Obsidian Entertainment\Pillars of Eternity (made backup of loadedsave.zip) folder and delete all saves but the most recently modified one in the user/saved games/pillars of eternity folder, then started the game once and placed the backup of loadedsave.zip
and it now works like it used to. I reccomend you make a backup of all your saves just in case the most recently modified one is the one corrupted.Also ive noticed that skipping the logos at the start of the game with LMB 9/10 times resulted in the game not recognising my save files, try the space bar instead.Beyond this I have no idea what is there to be done.