Kaphotics already explained to you earlier on: GBA/NDS will correctly assign stationary encounters with Method 1 IVs, However emulators cannot accurately assign the IVs from Method 1 in time, so the Pokemon will end up with Method 2 or Method 4 IVs. Method 2 or Method 4 IVs are incorrect for stationary encounters. So if you want to fix your Pokemon, assign Method 1 IVs to them.
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