Wouldn't it be possible to do this:
-Trade all your Pokemon to a friends device (or another game or something)
-Restart the game (as in actually restarting from Littleroot or where ever your game starts and not just soft-resetting)
-Trade your pokes back
-Get to the part with kyogre/groudon/legend of your game or delta episode
-Recatch the Pokemon
Would this work? It seems strange to me if it would, since people could end up with tons of deoxys, for example, and they wouldn't be special anymore. Is there anything that would stop it from working?