Can't help you with what the problem is, but you can save more than just using the autosave, you know. Try to make a full save (not a quick save) before starting each mission and when entering skyhold or each major zone. Try to keep 5-10 rolling full saves. Then you can load if bugs like this happen, and try to different things to experiment with getting past the problem.
Losing 20 hours and a full character because of 1 bug due to not saving is crazy. Just be thankful you weren't 60 hours in and on the final mission.
Well I do have a save and I could just ignore it but I actually want to do the mission? It does seem like an important one?
