I live in the Sierras in northern California and have flies bad this year too. Live rurally and a few neighbors have large livestock so lots of flies. I have the rubber interlocking mat flooring in my coop and scoop poop first thing EVERY morning with a huge metal dustpan and 6 inch putty knife, very effective. Then, just cause I'm a freak, scoop throughout the day to minimize poop within the coop. Any litter methods just gross me out, personally. Also use Coop n Compost and do properly compost. My older birds get to roam the property for most of the day and poop wherever, that I dont pick up which attracts the flies here. The flies are on my birds and bite them. Dont know what kind, dont care. So I understand PixieChick19. There have been posts here on BYC that swear by those yellow vanilla scented cardboard tree shaped car air fresheners. Hang several all over your coop/run, etc. Its supposed to repell them. Got a few packs and hung em in my coop and theres been less, not completely gone but sure smells nice! Maybe it'll at least help your situation. Much nicer smelling than the fly bags 
Im still looking for other repelling options for both keeping flies off my birds and away from my coop/garden area. Let you know if I come across anything else useful. Good luck!

Im still looking for other repelling options for both keeping flies off my birds and away from my coop/garden area. Let you know if I come across anything else useful. Good luck!