Koboh Devastated Settlement Puzzles - Orbs not present/never loaded in by game

I have the exact same problem as OP, and there is no orb to be found. We both did exactly as the game intends, we squeezed through the gap, pulled the box from up top, turned the gear to melt the goo and the orb that is behind the goo normally is simply not there. I even make backup saves and used one from before I entered the area, and there was no orb there then either.