Several weeks ago I remember someone else reporting exactly this same sequence. You can probably do a keyword search for Ohdaving. Although sometimes sorely tested, I never stopped in the middle of a crucial individual quest because I was afraid something like this would happen. I hope someone has a solution for you (other than the "load an earlier save" drum beat).
Oh, & save more frequently. I ran 2 save files, minimum, & would switch @ the beginning of each gaming session. Despite the somewhat misleading advertising, you must play this game with caution & foresight if it's important to you that you platinum.