I would recommend using the Repair app to keep track of the repair, including the Invoicing to the Customer for the replacement.

Helpdesk integrates with the Repair app.  

Repair orders can add the used item to your Inventory and issue a new item from your Inventory.  The serial numbers of both are entered on the Repair Order, which is created from the Helpdesk ticket and linked to it.

The Invoice will be just for the new product, but users can edit this to provide a discount for returning the old product, or the entire Invoice can be credited to provide a refund for part of the cost - representing the cost of the used item that you are giving back.