A negation of an artifact undoes everything that happened that phase because of it. If it's negated during battle, it does reverse effects from battle. After battle, it's too late, since it's a different phase.
Altar of Incense is in a different boat though. It grants Heroes protection. A protected card cannot be targeted at all, so if something like Wrath of Satan is played ("Discard all Heroes in play."), it can't even try to discard OT Heroes with Altar up. They're just not a valid target. So if Altar of Incense is negated after the fact, it's too late; Wrath of Satan already chose its targets.
