The first step is to eliminate potential sources of flies in the home. The toilet does not produce flies, and there should not be flies or fly eggs in human waste. That means the flies came in from somewhere else. Fruit bowls are a big culprit. Once in the home, flies will be attracted to the toilet, where they lay eggs and multiply. Before leaving your cottage, eliminate all possible sources of flies, including garbage (not even an apple core should be left behind) or compost.
The second thing you do is make the toilet unattractive or unavailable to the flies. Clean the toilet very well inside, in every nook and cranny, with something that will kill fly eggs like a mild bleach solution. Water and vinegar will not work. Don’t get the fan wet. With the Nature’s Head you can remove the fan housing and hose it all down outside, after using the bleach. However, the Separett fan housing is a bit of work to remove, so it’s best to clean the toilet with the fan housing in place.
Add about 5 cups of diatomaceous earth to the new coconut coir in the Nature’s Head, or with the Separett add a cup per week to the removable bucket. You may have to experiment a bit for the optimal quantity. Diatomaceous earth is a naturally occurring, soft, siliceous sedimentary rock that is easily crumbled into a fine white to off-white powder. It is a very good natural insecticide. This will solve the fly problem 99% of the time. It is not expensive and commonly available.
Be sure the fan screens are clean, unobstructed, and pumping air. You should be able to feel air being blown out at the exhaust vent.
As a very last resort, you can put a small “mothball cake” in the lower part of the toilet. The fan should exhaust the odor, and you should not smell mothballs in your home. This will definitely stop all flies. However, mothballs contain a chemical insecticide, and therefore must be used cautiously.
Once you do these things, I am quite sure you will have no more fly problems. Cleanliness and removing the source of flies is by far the most important step.