09-17-2012, 08:55 AM
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They are just going to turn into more flies. They're a normal part of the life-cycle of flies and they need moist soil and manure (not just urine) to live.
I would put down some Sevin Dust or Malathion to kill them. Then I would spread down some lime and cover up the hole left behind with gravel.
Sometimes, you can 'talk' a horse into peeing outside of their run-in by putting a pile of dirty old hay or shavings just outside of it. They want to pee in a bedded place, even if it is bedded with manure so that it does not splash on their legs. Putting gravel down there and bedding a different spot may do it --- may not. Old habits can be pretty hard to break.