If they have paid, you cannot send a revised invoice to deduct that postage, but you can just refund the cost in cash, when they come to collect.
Just mark the item as paid and dispatched the usual way, as dispatched is eBay's wording for a collected item. There is no tracking so you would have no proof the item was received, hopefully the buyer can leave you some feedback. You could print off a copy of the order details and have the buyer sign it as being collected.
You need to mark as dispatched through the Seller Hub only, now.
https://www.ebay.co.uk/sh/ovw
@270gemma