The team is aware of an issue with NPCs spawning underground and looking into it. I have passed on the information here about the NPCs showing up as invisible, as it could be related!
If I had a third hand, I'd give you three thumbs up..
I should add that folks on Reddit said that a botched pickpocket-attempt on a "missing" character can cure this... but I haven't tried this myself yet. Bareki eventually reappeared after traveling back and forth between maps a few times. Fast traveling back and forth while staying on the Lower City map did not seem to help.
