PokéBase - Pokémon Q&A
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Does it make any difference or is Hyper training just for making the bad IVs a bit better?

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You could say that Hyper Trained IVs are situationally better because they let you have any Hidden Power that you want without restricting your IVs.

For example, a Pokémon with Hidden Power Ice can have a maximum if 30 Attack IVs (iirc), but with Hyper Training you don't have to lose that extra stat point.
breeding will use the ivs not hyper trained stat

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Rather than actually changing a Pokémon's IVs, Hyper Training sets a modifier for the game to treat that stat as if it had an IV of 31.

In other words, they have the exact same effect on the stat.
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