You should be fine. This happened to me as I decided to upgrade the hard drive. I cancelled the original order and was basically immediately able to reorder the corrected configuration/discounts. No problems.
At one point however I inadvertently had two configurations in my basket and an error immediately popped up indicating only one laptop purchase per year with edu discount, please remove one item. However, as someone else mentioned above though (Post#4), it looks like you can purchase multiples as separate orders. When I just tested this and tried to place another order it basically let me with discount (although I did not click purchase). So you can also just try rebuying it first with the corrected specs and then cancel the other order after it goes thru if you are concerned.