The flies are an annoyance to us, but I don't think the torts even notice them. The only harm I know of caused by fungus flies is that their mobility allows them to spread vascular wilt diseases, affecting seedlings and plants, from one area to another. This, along with the annoyance, is why I use insecticides to eliminate the flies in my houseplants. You can't poison the substrate in your tortoise enclosure in the same manner. Diatomaceous earth, if it is effective on the flies, would be a safe treatment to use in your enclosure. I haven't tried it because I also have earthworms in mine and wouldn't want to harm them.
