PokéBase - Pokémon Q&A
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Here's what happened.

My Drifloon in Alpha Sapphire had a 4-heart affection, with fullness and enjoyment maxed.
I deposit it into the PC, send it to Pokemon Bank and subsequently transfer it to Pokemon Y (back to its original trainer).
I start the game in Pokemon Y, not moving Drifloon around at all, do a few minor things like Loto-ID and buy a few things in the game.
I save the game, send it back to Pokemon Bank and back to back to Alpha Sapphire.
I withdraw Drifloon back into my party and open Pokemon-Amie.
I find that its affection now is reset to 0, and fullness has dropped by one.

What happened? I have a Crobat that was maxed affection (and fullness and enjoyment) who followed the exact same path as Drifloon, and its stats did not change. According to Bulbapedia, transferring Pokemon through Pokemon Bank shouldn't affect a Pokemon's Affection towards a given trainer.

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3 Answers

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I'm not sure if this is true, but I think that with some Pokemon, if you travel with them for a while their Affection, Fulness, and Enjoyment go down, and after that, you must raise it back up. That seems to be what happens to me. Did you do anything immediately after you opened Alpha Sapphire, other than check Drifloon? I'm not the expert on this stuff, but I hope I helped!

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Affection is not supposed to go down when you travel, or over time. At least, that's what Bulbapedia says. Fullness does, but I don't know about enjoyment either.

As soon as I opened up Alpha Sapphire I immediately withdrew my Drifloon.
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You must have done something abnormal, probably on the transfer. Or you are looking at a different drifloon.

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I only have one Drifloon, and I did everything exactly as described in my post. This happened in a matter of minutes.
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Whenever a Pokémon is traded or PokéBank'd over to a person with a different Trainer ID, all Amie affection will reset. I believe that Drifloon lost affection not by being put in PokéBank, but being deposited in a different game than it originated in.

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I will test this myself and edit my answer according to my findings.

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The Drifloon originated in Y, but I increased its affection in Alpha Sapphire. Isn't it supposed to retain its affection when traded back to the trainer in which the affection was increased in the first place?
I have a copy of X and Alpha Sapphire, I'll try it later today.

EDIT: Ran out of time today. Will test tomorrow.
Any news? I've been moving my Pokemon around and not really paying attention but it seems a lot of my other pokemon seem to retain their affection, even though I'm transferring to and from the games which the Pokemon did not originate.