I haven't flashed a Hanso tune, I flashed one from the TuneECU website. I didn't ask the dealer one way or the other, but my dad had his bike fixed on warranty after flashing tunes. The only thing you would need to do is flash a stock tune when you took it in, I don't think they would dig that deep.
That said, I honestly haven't found a tune worth flashing, though I've yet to get one from Hanso because he's laid out. I'm thinking I'm going to buy a Power Commander.