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I own a copy of Omega Ruby, to which I've just Pokébanked all of my X Pokémon. Among them was a Latios, much better than the one I got in-game. My plan was to offer up the crappy Latios (sorry bud, I still love you) for a Latias on the GTS. But I wanted to make sure that the imported Latios would still activate the Eon Flute. So I released the dud Latios and successfully used the Eon Flute. Now that my curiousities were sated, I soft resetted the game to get the dud Latios back. Then I put him on the GTS and asked for Latias.

There, now I've got the backstory out of the way. My question is: Once I have both of the Lati twins, which one will be summoned by the Eon Flute? Will it be random? Will it be whoever's first in my PC? Will it always be Latios, since he's the one exclusive to Omega Ruby?

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Omega Ruby will only accept Latios for the Eon Flute.

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Latios is not exclusive to Omega Ruby. I know, because I've got Alpha Sapphire and I have both Lati Twins. I caught them legitimately in-game; I did not trade Latios over from another game; and I did not cheat to get him.

In my experience with Alpha Sapphire, you have to get an Eon Ticket. Talk to your father, Norman, once you do—he'll take you to a ship which sails you to the place where Latios awaited in my game. I assume it is the same with Omega Ruby, except that rather than Latios being there it will be Latias.

Anyway, to answer your question, I have always had Latias answer my summons when I played the Eon Flute. I don't know whether it is just programmed like that, or something, but that's what happens to me. I presume it is similar in its counterpart game.