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I have Omega Ruby and have Latios and my friend has Alpha sapphire and Latias. If we trade each other our Eon Pokemon will we both still be able to fly with the Eon flute?

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Probably.
Isnt an eon flute used to make arceus
That's the Azure Flute.

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Yes, it will always be the Pokemon you got on southern island.(source:expirence)

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