I use to use AR to catch modified Pokemon that was not in the game for Pokemon White 2, would they be considered hacked? Another question... I used the cheat to see all the Pokemon in the Pokedex so I could catch Shiny Haxorus... With using these codes cost me from transferring my Pokemon into Pokemon Y?
Assumingly, if the Pokemon is legitimately in every statistical way, it should be ok.
For the ones caught through AR, its hard to say. As long as the location data matches up, you should be fine, however, that's assuming that Bank doesn't know which game caught it. I mean, it will know which game is the one transferring, but if it doesn't know from which game a Pokemon was caught, you should be fine.
I don't believe the save file keeps track of AR usage. They're really only trying to keep Pokemon that were obviously hacked off the service. If you caught them just to catch them, I don't think there will be a problem, but we won't know until then!
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