So while they are irritating us and we want to keep them away, it is even more important to keep them away from your rabbits. Which in order to do this, means cleaning, and often. Several species of flies lay eggs that can hatch in under 20 hours. That means if you cleaned your cages yesterday, you could technically have maggots within a day. I don't know about you... but I hate maggots. With most of our rabbits we can go a couple days without too much mess. But with a cage of juniors it has to be a daily cleaning event. A doe with babies, it has to be a daily cleaning event.
I found a couple gruesome articles on what happens with flies and rabbits. I know a lot of people think they are safe because they are clean or because they live inside. Think again. Flies can lay eggs not, in the feces, but in the cage. Or even by the cage. Just waiting for a host. If it lays them inside a cage of one rabbit, that rabbit gets to be the host to all of it's larvae. Photos are fairly gruesome so don't read if you have a weak stomach.
A thing to mention is that many people believe Bot fly is not in our part of the US. However, a close friend of mine has known someone last summer who had to treat their dog for it and they never left the state of Utah. So clearly the flies live in our state. In fact it is native to Utah, known as the Warble Fly.
This site has a multitude of information regarding flystrike.
I like to think the more educated we all are the better off our rabbits will be as well. I routinely inspect each of our rabbits in a multitude of ways as a preventative. I know the behaviors of each of our rabbits, so if one is acting off, I can inspect any cause immediately. I check litter pans regularly for signs of blockage, or runny stool, or even no stool. I inspect the genital area for any signs of VD. Also as a preventative I like to mist the rabbits and wipe down their coats on a regular basis. They actually seem to enjoy this as well, especially during the heat.