I was playing a co-op run as a guest with the final Bunker quest in play. We paused and quit the run for a couple of hours then went back on to continue. My quest has Bunker had disappeared. When we finished the run, I have 4/4 for Bunker in the character archives, no final quest for her in the quest list but the skin is still locked in the character customization menu. 

Have tried a bunch of stuff including rerunning to see if the quest could still be in play but to no avail.