Are flies safe to eat if they are accidentally swallowed?

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Definitely! Flies and other bugs are actually quite nutritious to eat. They are lower in fat and higher in protein when (respectively) compared to meats.

You've probably eaten more than a couple flies in your lifetime without knowing. Research says that most people unintentionally eat the most bugs while sleeping. Many have also probably eaten food that flies have landed on at one point or another. Flies usually leave residual fluids on food they land on, but these quantities are so small that it will do nothing to the human digestive system. Your body will be able to easily ignore the trace amounts of bacteria left by the fly (or on the fly if you're eating it). 

In rare cases, if a ton of flies are landing on the food for long periods of time then you might want to think twice before consuming it. Also, you should avoid eating buckets of flies since they are known to be disease carriers. In very rare cases you could get a cold or ill. Medicines like penicillin will easily kill these bacterias though if the circumstance were to arise. 

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