I mean once the transaction was completed, that's your responsibility over, isn't it? I guess it's POSSIBLE that they left it in the shop after they paid for it, and then someone else pinched it, but even so, that's on them and not your responsibility to replace it.
I guess you either such up the cost and replace it as a gesture of goodwill, or stand your ground and refuse - and then like Music says, potentially take the hit.
If you've got a good reputation generally I think I'd take the hit. If I saw a customer review moaning about what has happened, followed by a reply from the business explaining what happened, I wouldn't think poorly of the business for it.