Flies won't hurt anything, they're probably drawn by the scent of the compost, but it may or may not be the urine. We add urine to ours too, and the chemicals are all neutralized in the process. If the flies lay eggs that hatch out into worms, they'll work on breaking down the compost too. As long as it's outdoors, you're going to have every imaginable creature hanging around looking for something to eat. My cats love to sit on the top of the compost bins and wait for mice to get close so they can pounce on them. We just don't worry too much about what gets into the compost, it's all going on the garden beds and all those same creatures will be flying/crawling/slithering around there too.

Cheryl

There are a lot of people that think javing flies around a compost pile is okay, but it is not. The majority of the time those will be the common house fly and those common house flies spread disease pathogens and should not be encouraged tohang around. The presence of flies indicates a too moist condition in your compost pile, the eggs need that moisture to hatch and the larva need that moisture to live, so turn the compost or add some dryer material and eliminate the flies.