I would do a second invoice and a credit note, then apply the credit note to the new invoice. Put the new item on new invoice, and old item (returned item) on the credit note.
If the new item's price is more than the old item, the new invoice will be 'partially paid' status after the credit note is applied.
If the new item's price is less than the old item, the new invoice will be 'fully paid' status after the credit note is applied. And you can still use remaining un-applied amount on the credit note to some other invoice in future for the same customer.