Everytime I defeat John and liberate the valley, the red silos disappeared and I was greeted for completing a mission I did not even do. I never even touched these silos and wanted them to remain after I liberate the valley. Is there anyway to fix this?
It sounds like this may be an issue with your save file - the red silos are meant to be destroyed by you at some point but not on their own. Try reloading a previous save to see if this issue persists.