Customer credit for partial price returns an item to stock

I sold some items with an agreement to cover a portion of any repair costs, if there were any. Four of the items required a small amount of repair, so I issued a credit note for partial costs on those items and the customer paid the difference. But the credit returns these items into stock!. I cannot issue a credit with a zero quantity so how can I assign the amounts to these items to get the true picture? I can't change the original invoice because it was in a different VAT quarter. I could void the original invoice and reissue but that isn't how it happened and payments were made and assigned to the invoice before the repair amounts were known.