If you haven't yet issued an invoice, you can discount the postage component to zero so that the invoice total is only the $2.50 that the buyer will be paying for the item on pickup, as FVF will be charged on the total amount paid by the buyer.
The customer is going to pick up and you are worried about about paying % for postage? What about the buyer paying $8 for postage that is not going to be used?
I suspect the OP is mainly concerned about paying FVF on the postage component which he won't be charging the buyer. As he should be, as 9.9% of $8 will wipe out almost half of the minimal profit that he'll make on a $2.50 item.
I had a similar experience the buyer somehow checked out the eBay invoice as paid but came over and paid cash for the item less shipping . That was fine buy me ( no pay pal fee ) but I was slugged FVF on shipping So I sent an mail to eBay requesting a refund . Happy ending I received the refund
