Do you have an other incubator that you could move the viable eggs to? I would spray them with some sort of egg sanitizer (yeah, I know that's a no-no) and move the eggs out of that bator, and set them up in a new bator. I would then vacume it out, and completely wipe it down inside and out with a good bleach and soap solution. Does it have a fan? If so, I would turn the fan on, and completely wrap the bator in plastic. Leave a bowl of strong bleach solution in the bator. Let the fan run for 8 hours or so. I suggest that you do this outside your home.
Those flies are a cess pool of bacteria. I am surprised that you have any eggs that hatch at all. Any chicks that do hatch are going to be maggot food. The flies will be attracted to the moist chicks, and will be laying eggs on the chicks. Fly eggs hatch incredibly fast. The maggots will immediately go to work devouring the chicks.
Before committing eggs to that bator again, run it for a day or two, perhaps putting something in there that would be an attractant if there happen to be any lingering flies or maggots.