Unfortunately, having a fenced yard doesn’t mean that bunnies will be safe. Predators can jump or climb over fences, can dig under fences or can fly in and attack a rabbit. A rabbit can also dig out of a fence. I know someone who was near her rabbit in a fenced yard, and a hawk flew in and attacked her rabbit. I also have a friend who recently lost her rabbit to a combination of warbles from the bot fly and possibly ingesting toxic plants in a fenced area in her yard. She was and still is devastated about the loss and thought that her rabbit was perfectly safe in that fenced area adjacent to her house. Her rabbit loved that area and had such a good time out there, but my friend will never let another rabbit go outside.
I’m sure that your rabbits really love roaming around the yard, but I don’t know of any preventative for the bot fly, and with the other dangers outdoors, it really is far safer to keep rabbits inside.