No they won't, you'll have to place a new order. For some reason the edu and normal sales systems don't talk to each other(or at least they never have when I've tried the same thing, they always end up creating a new order) Worth doing though, £40 isn't a shabby discount.
Well what do you know.
I called Apple up this morning about this issue. I told them my order already shipped (since it's actually on the truck to be delivered today), so instead of making me do a return, they will just credit me the $45 difference (and tax), plus the $19 I paid for overnight shipping. That's just incredible which means $66.83 back to my card. I'm quite happy with Apple about this. Makes me want to buy another Mac damn it.