Well, depending on how it's cut, it should still work, actually... if you cut it in the right place, then all you'll be doing is disabling the final 8 channels and changing a x16 card into a x8 card, which doesn't actually impact performance because the PCIe bus bandwidth is not the bottleneck. Tom's Hardware did a test a while ago where they didn't cut off the card itself, but taped off sections of it, effectively turning a x16 card into a x8 card, a x4 card, and even a x1 card.
My computer, because I got a Dell SC420 (it's a server; not intended for desktop use) only has a x8 slot and no x16 slot, so I had the option to either cut off part of my card or to cut the end of the slot itself so that I could fit in a x16 card; I opted to cut the slot and not the card (it was easier; the card is tough!), so I currently have a x16 card running in a x8 slot. But I did this with an inexpensive ATi card (x300SE [without HM, thank goodness]; cost my only $40 USD because I got it refurbed) because I'm not a gamer. But when you are dealing with one of those ridiculously priced card that cost more than what I paid total for my entire system, then that's a different story.