You can't - the delivery method can only be selected by the buyer where available through checkout, or altered by the seller through an invoice; invoices can only be sent after a buyer has purchased an item but before they have paid. (Refunding postage costs won't change this, I'd normally refund less fees incurred, though).
In this case, I would just mark it as shipped - maybe send a quick message to the buyer (just to avoid potential confusion on their part) that you are marking the order as shipped so that the order can be archived, and to ignore any dispatch notices they might receive from eBay.
