Forum:Magician Navigation + Metal Reflect Slime

So me and my buddy were just going a round and this is what happened: i activate magician navigation on his turn, he activates MRS. Now it's my turn, I activate Navigation's second effect to negate MRS until end of turn. I assume the monster just "disappears" til the end of turn since it's root is negated, but he believes it wouldn't effect the monster since it was already special summoned. Any insight?