Interesting glitch there. However, if it only applies to the Legendary Zapdos, it's only useful for a New Game+ run, since you only get this card after finishing the game. It might be that the programmers messed up when a card is knocked out by PokePower damage, though. By looking at the card list, Gengar has a PokePower that can knock out opponents, it might be a good idea to check if the glitch works with Gengar, too.
EDIT: The glitch is real! Apparently, the problem is that, immediately before the game displays the Decision... screen, after you've won the match with Zapdos's Pokepower, it saves an invalid state in Continue Duel.
I managed to do two curious things: the first, as shown in the video, is to battle an opponent with an empty arena, if you just finish your turn without attacking, you just win the game immediately. But by attacking the opponent, the game starts to think they have a pokemon and the duel gets completely glitched.
The second thing is to do the Zapdos glitch when you pick up the last prize, if you do the glitch you will continue the duel with no prizes to pick. This doesn't look exploitable, though, since if you try to pick up a prize when there are none, the game just gives you the victory without any bugs.
My feeling is that the game does this invalid save at the end whenever it is still your turn to play. Probably, when you issue an attack command, the game immediately changes to the opponent's turn, and if you win the match with an attack, this wrong save is avoided. However, by using a pokepower, it is still your turn, and the game performs the save.
EDIT 2: My theory should be correct. I managed to do it with Gengar!
The thing is, in order to use Gengar's Pokepower, the opponent needs to have more than one Pokemon, so the only thing we can do is get a duel with zero prizes. Is there any way to exploit this?
EDIT 3: I finished testing, and unfortunately I have to conclude that the only way to exploit this glitch should be with Zapdos. The bug occurs when the duel finishes midturn. the only way to do this is by using PokePowers. If the duel finishes by any player running out of cards, the state you get with Continue Duel is perfectly valid, and no corruption should be possible.
If the duel is finished by running out of prizes, the game handles correctly the case when zero prizes are on the field. Initially, I thought I could make the prize amount variable underflow to 255, but that's not possible, the game saves which prizes have been picked with a bitmask, and calculates the amount of prizes left by counting the number of 1's in the byte.
The pokepowers that cause damage are those of Zapdos, Gengar and Machamp. Machamp's is useless because it happens during the attack phase and the invalid save doesn't happen (I tested). Gengar's pokepower needs more than one active pokemon to be used, so it can only glitch the prize amount.
The final possibility without Zapdos is to lose the duel before the attack phase. Since running out of cards is no good, we need to KO one of our pokemon without an attack. Sadly, no Pokepower allows this. I even tried something very exotic, like putting Gengar against Machamp, and damaging it with Gengar's power to see if it would counter and kill me. Unfortunately, that doesn't happen. Machamp doesn't counter Pokepowers.
So, unless I am missing some key mechanics here, the only way to exploit this glitch would be with Zapdos. Maybe it works in Pokemon TCG2, where you get the card before the end of the game?
