You shouldn't need to add the 3.4% to an invoice for the Shipping cost, as Paypal would have taken that amount off anyway had the original buyer waited for the full invoice.
But do add the 20p as you get charged that as a minimum per transaction.
You can refund and send an invoice from ebid that includes shipping as the only part you will not be refunded is the 20p flat non-refundable fee taken by Paypal.
just remember to add that non-refundable paypal fee onto your new invoice.
Jason