Uh oh...I had phorid flies last year to get attracted to my eggs. And while initially interested in the fungusing/dead ones...I went on vacation thinking "Bad eggs don't hurt good eggs". I removed the dying/dead eggs and thought the problem would correct itself. No dead eggs, no flies.
While I was gone, two clutches were supposed to pip, they were late and should have pipped before I left really. But I thought to myself, "Self, you leave them in the container together for a week to shed anyway, they'll be ok." I just put in a small water dish and left them be.
So a week later I came back to find hatchlings and pipplings having been eaten alive by maggots. The flies must have laid eggs on the pipping snake eggs (they do smell like decaying bell peppers), and if its warm enough fly eggs hatch in a few hours time and they began to eat. They ate 20+ hatchlings before they even had a chance. I got home to see the destruction and to have to euthanize two gorgeous motley babies that were somehow still alive, but had a gut full of writhing maggots.
To be sure, are they fruit flies or little black flies?
Fruit flies have a striped abdomen and the classic red eyes.
The little black flies could be Phorid flies, which resemble fruit flies very closely, although they lack the red eye and are slightly humpbacked.
Phorid flies are attracted to decaying organic matter. You can tell if they're Phorid flies by the manner of their habits, when you shoo them off, do they run a short distance before taking flight? If so, they're Phorid flies. All other flies will immediately take flight.
The best advice I can give after having them decimate two clutches of pippies last year, is to cover the air holes on your incubating boxes. If you don't want to do tape, maybe Elmer glue a patch of paper towel/coffee filter over the vent holes if you're concerned about airflow and see how that works. Then try to limit their food and breeding sources and curb their population.
Here's an informative page about Phorid flies, just ignore what they try to sell.
Phorid Fly Information
Fruit flies can be attracted to a trap, which I purchased, as they're attracted to our undercabinet compost container that we put in scraps of organic material destined for our compost pile. The trap worked really well, its filled with vinegar which the fruit flies are attracted to. They go in the cone shaped holes and can't find their way back out and end up drowning.
Fruit Fly Trap
Hope that information helps a little bit.
. They seem not to bother the healthy eggs, but I'm not about to experiment on how long it will be before they do. I found a couple of different suggestions googling it, such as this...
