The eggs sinking in is the classic sign of dehydration. Are the eggs in closed containers or are they open to the air in the incubator?
If the cups are open, I would start over with a fresh mix of incubation medium and bury the eggs till only a trace of the top surface is visible. And I'd either seal up every hole in the incubator or put the egg cup in some sort of closed box that fits in the incubator.
Good luck.