Update: I did not have the network drive problem above, but I did figure out my own trouble. It seems the some saves are getting bugged and trying to force themselves into the spot for the continue button even though they are not the most recent save.
To fix this go to C:\users\username\appdata\local\temp\Obsidian Entertainment\pillars of eternity II. In that folder there should be a zip file named "loadedsave.zip". Open it it up and look for the screen shot, that will show you the picture from the save, that's your bad one. Easiest "fix" is either to delete or move all but your most recent save from the saved games folder and delete that loadedsave.zip. Or you can keep loading the game and exiting then deleting until the zip file matches the most recent save.
Also make sure to turn of Cloud sync if you have it on so the do get put right back.
I hope this helps anybody else having trouble. Still not sure what causes the bad save in the first place or if its a bad save or trouble with the game itself, but i'm back up and running.
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Same issue for me. Saves seemed to reappear after I uninstalled POE from my laptop that was on the same network. I was able to exit and enter the game no trouble. But this morning it seems the problem is back. Saves are in the right location but are not showing up in game. For me it seems to happen around the 10-12 hour mark. Both games I've lost happened at different story points but around the same time frame.
