I'm personally not convinced that Hyper Training will actually overwrite the IVs. I think instead it applies addends to IVs, with further coding keeping the values from going beyond the IV31 level (or below the IV0 level, for that matter). If IVs actually were overwritten, it would lead to some...interesting...breeding repercussions (no more need to rely on others for an all-31 Ditto coterie!). It's also a matter of whether Hidden Power is still coupled to IVs; if so, I don't think too many players would be happy with finding that utmost perfection of stats suddenly means they don't have the Hidden Power they wanted.
In short, I think that Hyper Training increases will only apply to combat calculations, not stat inheritance or Hidden Power determination. That 4/28/31/12/9/30 critter you have will still be 4/28/31/12/9/30 after Hyper Training, as far as anything outside of battle is concerned.
In short, I think that Hyper Training increases will only apply to combat calculations, not stat inheritance or Hidden Power determination. That 4/28/31/12/9/30 critter you have will still be 4/28/31/12/9/30 after Hyper Training, as far as anything outside of battle is concerned.