Periodically, our master bathroom has swarms of houseflies, I mean hundreds in a day or so. We have also looked at the toilet for leaks but, again, it came up clean. The flies seem lethargic but look fully grown. My home has had the same problem with flies over the years, and after battling the problem, I have found some causes, solutions and preventives.
Litter boxes are attractive.
Because you mentioned the bathroom, I am inclined to believe the source of the problem is your drainage plumbing. Also, you may need to pour bleach down the drains. You might also look into the biological drain cleaners. Hope this gives you some ideas. Answer provided by Carolyn Krchma .