I'M SO MAD !! I went on Nintendo's server to use Pokemon Bank ( and add my gf with my other friend code because she doesn't have Pretendo LOL ) And when I came back on Pretendo's server, ALL MY BADGES WERE GONE!! I took soooo much time putting Badges around and it's all gone :,)
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lol
It's because badges are tied to the NNID/PNID that's in use, if you go back to nintendo network your badges should re-appear