Have they aready paid? Then, the easiest way would just to hand over the cash on delivery, as you cannot then change the invoice.
You could send a partial refund no benefit doing it this way as full seller fees have already been paid.
If they haven't paid you can send a revised invoice with a zero postage cost. Come back and I can explain how to do this if they haven't paid.
To finalise the transaction you mark the item as paid and dispatched. Dispatched is eBay's wording for a collected item.