Many years ago, I had a severe mite infestation in my coops. I sprayed Permethrin once a week for a month. I cleaned the coops prior to treatments. No more mites and a bonus, no more flies. If you use Permethrin there is no egg withdrawal period. I would spray inside the coop every nook and cranny once a week for a month. It will kill them as they hatch out.
Here is a mixture chart made by a friend. The lines marked in yellow worked the best.