You are not able to discount the item price after it has sold, and if it was free post you will not be able to include a discount on the invoice at all, as you can only discount the postage when invoicing.
In order for the item to sell and be invoiced at a lower price, the buyer would have needed to make an official offer via eBay by clicking "Make offer" on the listing, in which case you would have received an email giving you the option to accept, decline or counter-offer.
If the buyer offered you a price informally, eg just through messages, then clicked "Buy It Now" at the full price, there's no way to invoice at the lower price unless they are paying via PayPal and you generate an independent invoice (or another payment method which provides the facility to pay less than the eBay invoiced amount).
If that's what happened, and neither you or the buyer are comfortable with an independent invoice, bank deposit, etc, then you will need to cancel the original sale and relist the item so that they can formally purchase it at the agreed price. Keep in mind that you will be paying FVF on the current sale price, so if the difference is significant, you may want to go the cancel / relist route.
