1. The Factory spawning population - This is self-sustained, and never encounters radiation.
2. A subset of the spawned males from the factory population are irradiated, making them sterile.
3. The wild population, consisting of the sterile males + wild males + wild females.
If for some reason the sterile population is not fully sterile (unlikely), then maybe there is a gene that helps for radiation resistance, but the children of that strain will not encounter radiation, so it fades away.
The factories are not going out to the regions where the flies are deployed to get new fly studs.