I messed up on my Pokemon Pearl game and used the run through anything glitch with action replay caught Palkia not you know what to do they fight me now?

Using the run-through-anything glitch with Action Replay in Pokémon Pearl will not affect Palkia's behavior or cause it to fight you. Action Replay is a device used to modify game data, and while it can be used to obtain Pokémon and items that are not normally obtainable in the game, it does not change the game's core mechanics or AI. Palkia will not become aggressive or attack you just because you obtained it through Action Replay.