I have the same issue. I upgraded through AT&T to the 6 64 Space Gray, and the confirmation email said that it would arrive on/around the 19th.
Now the order status page is showing an estimated ship date between 9/23 and 10/2 and gives me the option to "Cancel Preorder."
I checked Apple and it shows the 6 64 SG as being available to ship and arrive on 9/19. So, now I'm wanting to cancel the AT&T preorder, but only if it will cancel the upgrade as well and then try it through Apple.
I just don't want to cancel the pre-order and then they tell me I still upgraded so it wouldn't let me try through Apple and I'd still have to wait (maybe even longer) with AT&T.
So it is a sure thing that if you cancel the preorder, it will update your account (eventually, at least) to show that you are still upgrade eligible?