If the buyer didn't go through checkout, the FVF won't have been charged on postage yet.
Probably the best thing to do now is issue an invoice to reflect the pick-up option, when you get to the invoice page, remove all postage options except one, then switch that to local pick-up (it's one of the last options in the dropdown menu) and enter 0.00 in the field for cost, then click send information (don't hit recalculate, as that reverts the invoice to the original). If the buyer didn't go through checkout, this may seem unnecessary, but it will ensure that if they do go through checkout later ot mark as payment sent, the system can't assume postage was paid
Make sure you message the buyer to let them know that the invoice is just for record keeping purposes, to ensure it's an accurate reflection of the transaction etc and not a request for payment, and once you've issued the invoice, mark the item as 'payment received' on eBay.
