The reason to open an Unpaid Item Dispute is to get your Final Value fees reimbursed and to give a strike to an unresponsive buyer. If i understand corrrectly, you were trying to be a nice guy and avoid putting a mark on your buyer's record once he got in touch and he agreed to pay the FVF.
"No good deed goes unpunished" is the moral to your story. Once you discovered you couldn't change the invoice amount, would have been the time to tell your customer that you regret you are unable to accommodate him. You shot yourself in the foot when marking the item as Paid.
You could send a PayPal invoice to them in the amount of the fees, but he is under no obligation to render the reimbursement. However, since you kept your side of the bargain and if he is an honest person, he might pay it. You have nothing to lose by doing so.
Most of my listings are BIN with Immediate Payment Required. For the few auctions, I open an UID a week after the sale. This gives stragglers plenty of time to pay. That's too long for some sellers, but giving the strike is a very important seller protection, one of the few we have. Sometimes a cancellation of a transaction is appropriate, especially when it is buyer requested, but it helps all sellers when an Unpaid Item Dispute is closed if they have their Buyer Requirements set to weed out dead-beat buyers.
