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@Deoxyz and @theSLAYER, I am being told it might have been only X, or only Y. So even though the cards have both games flagged, the servers only served a specific card to a specific game, and half were broken. I wonder if there is a way to prove this.

No, PKHeX doesn't do any 3IV collision detection as there's only 2 instances of this happening: When the internal event binary is built, the 3IV is included first, and the No IV is included second; Directory.GetFiles doesn't return stuff in a defined order. I've updated PKHeX's behavior so that it plays favorites with the worse of the two cards. https://github.com/kwsch/PKHeX/commit/16341b4d910c676e05663dd4b050fe53fba4b161

Because only the PIDIV algorithm is known; the species-PIDIV relationship isn't. It's best to positively recognize them as PCNYx, but not give fake hacks a sense of validity.