We use the 'deep litter' method in our coop/house and never have any problem inside the coop with flies as the chickens must eat the flies when in their larval stage.
My husband is a professional woodworker who has a shop next to our home
so we have a constant supply of fresh pine shavings which we add to the
coop/house area in the large black leaf size bags whenever we begin to get
a 'whif' indicating more is needed. We use pine straw from our yard in the nesting boxes and when that's dirty and I am replacing it I just dump out the
soiled bedding onto the floor.
I rarely ever have to clean off an egg before packing
it which always amazes me since there are 12 hens
and they only lay in 3 of the six nest boxes so pine
straw must be helping somehow.
Between the organic greens we feed them daily from our garden, the pine straw, the pine shavings and their poop and constant 'working it all with their feet' it just turns the consistency of 'sand on the beach' and when it gets
too deep for us to walk in it comfortably we shovel wheelbarrows of it out
and put it on our compost pile - let it 'cool off' for a year then use it on the
garden late winter to work into the raised beds about 6 weeks before planting the Spring greens, etc.
When we have chicks in our brooder box and they cannot get to the 'droppings' or the larve beneath the cage/brooder box ( we use a wire mesh as floor and the droppings and wasted food go under the enclosure ) then we do have flies.
I know it is hard to believe but this method has worked so well for us that
our chicken house/coop almost has a pleasant piney/earthy odor which is
not what people expect with chickens. - and the constant compost isn't bad either!
When cleaning out the coop/house if using this method it is imperative to
retain at least some of the deep litter as it is 'innoculated' with all of the
organisms that are necessary to make the whole system effective.
Thank-you mtnviewfarms. That was very informative, especially the part about leaving some litter when cleaning so that you keep some of the beneficial bacteria. My husband is also a woodworker so this is the method I am planning to use. Hope they don't get too spoiled with mahogany and walnut shavings, LOL.
I have horses and they are way worse at attracting flies than my coop.
The most benign (non-poisonous) thing to use are fly traps. There are several brands available I think I use one by Victor. Essentially they are a jar or bag that has a modified opening at the top and a loose 'hat' . You fill the jar part way with a fly attractant and water that drowns them once they get in the jar. You can hang the contraption in the hen house or barn and the flies go in but cant find their way back out because of the hat. You can clean them when they get full or just toss them and get a new one. Work great, zoos use them too.
You can get a hanging no-pest strip that is not sticky but rather emits the insecticide Dichlorvos. It is approved in livestock buildings where humans are present less than 4 hours. It has been around forever it seems but it is a pesticide, so be mindful of that. The strip lasts up to 4 months.