You'll have to send a new invoice for the whole amount. If the amount paid by the buyer already includes the postage, I'd just mark it as paid and confirm their delivery address.
If they haven't paid postage yet, you can send the invoice but just advise only the postage amount is due. (If they want to pay for postage via PayPal, you'll have to generate an invoice in PP and send it to their email address - just be careful how you word that if communicating via ebay as they're taking a particularly over zealous approach to any and everything that looks like it could possibly be talking about transactions outside of ebay).
