All negates undo an effect (SI lets you do it as the effect completes, but it is still undoing the ability). I'm not sure what you mean by differing from CoN, but this is triggered upon the removal by special ability. Once all abilities resolve, if it can activate (the battle hasn't gone to Battle Resolution by an End the Battle ability and Throne isn't negated), then it triggers at that point. Just like playing a negate at this point would undo the effect, so too does Throne undo the effect causing removal by negating it. Since it was undone, this generally means the character will be back in battle as it was before the ability.
