Well, you are now out the paypal 2.9% on that first payment. Check to see if the invoice option is now available. You may be able to use the drop down menu to select "unmark as payment received" and see if the send invoice option appears.
You need to send a polite message to the buyer apologizing for the issues and make sure they still want to proceed as well. They still may need to send full payment and you refund a shipping discount.
Remember when issuing the discount that you paid eBay and Paypal fees on the TOTAL amount including the amount you are refunding. When I refund for combined shipping I do not refund the fees that I was already charged.
Member of the Grumpy Old Man crew