Dreammaker
Songster
If removing the hidden, rotten eggs doesn't help, I had read about Little Trees Vanillaroma (yellow) car air fresheners helping with flies and thought it was ridiculous. But, I had more flies than I'd like in my chicken coop, so I tried them (cheap enough!). Surprisingly, I think they seem to be working! I also had been having issues with their bedding that was drawing flies in there which I've since resolved, but the Little Trees did seem to do something. As soon as I put one up, the flies left. I see at least 50% fewer of them now. I'm not sure how things would pan out with your duck coop, but you could give it a try. I just made sure to hang mine high enough that they wouldn't try to peck at it. Some folks with larger coops/runs have to use several; I just have one in my 6x5 coop. I think they only last about a month before you need to replace.
