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Thank you for your honesty. To an extent I feel the same way as well >< Even though I don't know how to debug XD, nor could I launch PKHeX on VS for some weird reason, I followed a hunch I had and found out what was wrong: The indexes for the data are off by 1. When I purified (81) Togepi in-game, (82) Poochyena appears purified in PKHeX. I purified (72) Lapras in-game, and (73) Lugia appears purified in PKHeX. So the issue with (1) Teddiursa probably means it's reading data from slot (0), or something akin to that.