Has your buyer paid any money yet?   just for clarification

You can also give a partial refund,  but if I do that I do it at the order level so it is spread across the 3 items,  Not against just one item.

If the discount is less than the postage cost, you can discount the postage on the invoice to get to the right total. But I would think you probably agreed to a combined postage cost as well. The only thing that can be discounted on the invoice is postage. Generally the easiest way is to create a Special Listing for Buyer XYZ with the agreed price plus postage (or free post if the offer included postage.) However you should have done this BEFORE you allowed the buyer to purchase the items separately. I can only suggest you cancel the original sales (using the reason Buyer request) and then create the Special Listing.  (Remember  to un-select the auto-relist option.) You will need to explain carefully to your buyer what you have done. Others may have a better solution.