Hey guys, sorry to hear you’ve had trouble with this.
Was just replying to another thread on this topic as well so I’ll post up the same info.
When you faction change multiple times it can have an effect on quests resetting (some but not all) and phasing too, which can cause issues where you have ! markers you can’t pick up, and ? markers you can’t go hand in because in the past you’ve already done it and the NPCs are no longer there.
It is something the Devs are aware of alright, but we can try to help as best we can in the meantime, might not be perfect but we’ll do what we can.