That's one of the problems with dc, no upgrade without going around in circles.
If your customer doesn't mind, you can invoice them through Paypal for the difference.
If your customer won't use paypal, you can cancel the order and have them repurchase at the correct rate...I think this is a horrible way to do it, very inconvenient for you and the customer, and a great way to lose a sale altogether.
What we are not supposed to do is set up a separate listing just for the shipping upgrade....This is what I would do with a customer who won't use Paypal. Yes, I do realize what I just wrote.