If there are 90 damage counters on a defending pokemon level X with 120 HP - If I use Gengars Level Down (from the bench) and reveal the pokemon underneath their level x that has only 90 HP. Does that pokemon get KO'd ?
Yes. After the LV.X card is returned to the deck, the resulting Pokemon is KO'd when the Power is finished (because it has damage on it that exceeds its maximum HP).