The 1st thing that comes to mind to me is to actually handle the collisions on both objects. The bullet can determine whether it should destroy itself or not, while the enemy it collides with determines if it can keep taking hits or not. The code on the enemy would set a variable, maybe a count down for a certain amount of time. Then it would check that variable before actually reacting to the collision. The event would still happen since the bullet is still there, but the reaction doesn't have to happen unless you want it to.
Just FYI, the reason I suggest putting this variable and control on the enemy, not on the bullet, is because that 1 bullet wouldn't collide react to the collision with the next enemy it hits as it penetrates through the 1st enemy if the bullet itself is waiting for the countdown, while the 2nd enemy would contain its own countdown variable.