The Sister Location animatronics were reprogrammed when the company was bought over, but the workers never managed to get the kill code out of Ft Freddy due to him killing them before they could do so. With the new upgrades they received and also new tech, the kill code began to adapt and upgrade on its own. Ft Freddy keeps it a secret because he knows that with how far its upgraded, his whole system would have to be reset in order to get rid of it.