Hi there.
Although flies can infest a wound and cause fly strike, I have never yet heard of flies carrying any disease that would effect chickens.. mine eat any flies they can. In fact flies, consuming and processing dead stuff may prevent disease... their like garbage collectors getting rid of the nasty stuff.
Some folks even make use of maggot buckets... attracting the flies to lay their eggs... then the chickens in theory eat the maggot when the crawl out of the growing medium and fall to the ground in order to pupate.
Keeping waste disposed of can go a long way towards keeping fly populations down.
I use bait traps... with screw on lids.. put something dead smelling inside like raw meat trimmings you were gonna toss anyways. They love rotting potato which smells just like death. The need to have enough warmth to really stew up the smell and plenty of water, moist stuff stinks worse than dry and the deeper water helps them die/drown faster when they get knocked down by others flying around.
If I have something dead or gross.. I will put it out to attract all the flies to and invite them to lay their eggs.. which they happily comply during the all day warmth... at dusk they disappear and I dispose of the fly blown whatever... bagging it tight or burying it deep so the babies never hatch at my place... they might hatch in the bag at the dump but doubt they can get out!

(to the flies).
Also when they do disappear, they are sleeping somewhere near by. I use a Permethrin based horse fly (and premises) spray... on the walls, roost, etc as it also fights mites and lice. The main reason I bought it was to keep mosquitoes off my dogs. But it's very effective at treating many things when used according to directions. It IS labeled for use in chickens.
Humidity always increases fly activity at my place... like when I use the hose in the mornings and the ground is wet. Keeping things dry can help. Sometimes I use PDZ on my droppings boards etc. I'm not a fan of DE plus it's ineffective in my environment, so avoid that at all cost
Hope this gives you some ideas!
