Because the damage was done when the ammonia climbed to 2.0 before you added prime the first time. Ammonia will give the corals a chemical burn, so think of it this way... if you were put in acid then it would burn your body. Even if the acid was then neutralized the damage would already be done and you would still have acid burns on your body that would take time to heal. If the acid was weak (low levels of ammonia) then the burn wouldn’t be too bad and wouldn’t take too long to heal, but it would still take time. If the acid was strong (high levels of ammonia) then the burn would severely injure you and take much longer to heal... or it could even kill you.
All you can do now is keep the ammonia neutralized so there is no further damage and allow the corals time to heal on their own. Their stress response is to close up while they heal, so they will stay closed and not look well until and if they are able to recover from this.