The flies you're talking about are in the family Phoridae, the so-called scuttle flies, named for the way they move when walking. Males are much smaller than females. Females are about the size of Hydei fruit flies.
Phorid larvae eat virtually any organic material including decaying plants, insects and animal matter, and also will attack reptile eggs, chewing into the shells and allowing the eggs to bleed out and die. Typically, eggs at the bottom of a clutch are killed before eggs toward the top of a clutch--when considering adhesive eggs.
Phorids are everywhere, like bacteria, and are not transmitted by dried sphagnum moss. The Phorids that have attacked your snake eggs were most likely in the house, in the snake cage, and fly eggs were probably laid on the snake eggs before you removed them from the female snake's laying box. Once in the incubator, the fly larvae hatched and burrowed into the eggs.
Insecticides like Provent-a-Mite may be effective in killing flies or larvae which come in contact with the pesticide, but Provent-a-Mite is safest around reptiles once it has dried out. Moist conditions inside an incubator may allow toxic chemicals to transmit across the egg membrane and have some effect on developing embryos. The effect of pesticide poisoning may not be immediate; long-term effects might include nerve disorders later in a hatchling's life. Although I have not heard specifically of any detrimental effects of Provent-a-Mite, I note that the label advises allowing the pesticide to dry completely before exposing live reptiles to it, and pesticides in general are best avoided around any moisture-dependent living things like fish, amphibians, and, IMO, reptile eggs.
To defend against an infestation of Phorid larvae in an incubator, I place freshly laid eggs in a clean jar with a bit of moistened paper towel on the bottom and watch the eggs for about four or five days to see if any fly larvae appear. If they do, I remove them manually with a small watercolor paintbrush or just let them crawl off the eggs at random. If I find fly larvae I keep the eggs out of the incubator until I'm satisfied I got them all.
I monitor the eggs closely for several days after placing them into a container of moistened sphagnum to be sure no late-emerging fly larvae escaped my scrutiny while in the paper towel jar. So far, this system has worked perfectly for me.
Though not always successful, I try to keep Phorids out of my snake cages in the first place, and watch closely when female snakes are laying in case I spot some flies around. If I see flies anywhere near a laying female, I'm extra vigilant while the eggs are in pre-incubator quarantine.
If you want to clean batches of sphagnum for future use, you can place moistened sphagnum in a freezer for a while, at least a few days, which will kill any insects, their eggs and larvae. I also put the sphagnum-filled jar in the sun after taking it out of the freezer to further thermal-shock the contents. Then I just leave it closed until I'm ready to use it.
I'm not in any hurry to get eggs to hatch so a few days delay while I verify there are no flies present is fine with me. If the eggs are clean when they go into the sphagnum jar there are no further problems as far as insect damage.
I don't breed snakes every year but over the last 40-plus years I've hatched thousands of snake eggs from many different species. By far my most successful incubation method has turned out to be simply placing snake eggs into a large jar half-filled with clean sphagnum moss, moistened with distilled or reverse-osmosis water. I usually just put the egg jars on a shelf where they won't get too warm and leave them be for about 8-12 weeks. Temps are generally around 78 degrees.
