The flying gene is surpresed, not totally wiped. People get "flightless" fruit flies through selective breeding. They take out any mutations they find within their fruit fly culture, and breed the mutations only with the other mutations. This usually causes then to loose the ability to fly. Like curly wing flies. But when given subsequent resources (i.e. food, water, HEAT, etc...) the parents will bear offspring with the ability to fly. To help slow down the process of the ability to fly, I suggest keeping your flies in the coldest part of your house. 60s (Fahrenheit) should do the trick, but wouldn't go lower than 62F, or higher than 70F.
Where as there is also the very real possibility of wild fruit flies making their way in. Have you seen fruit fly eggs? They are small. They can make there way through some of the finest meshes.
One way or another one day YOU WILL eventually see one of your cultures regaining the ability of flight.