This is the procedure we follow.

1. Create a sales order
2. Create a delivery order from the sales order
3. Complete the delivery order
4. Go back to the sales order
5. Create the draft invoice
6. Edit the invoice to show all parts delivered and add a note as to why the invoice why canceled.
7. Save the invoice
8. Cancel the invoice (the invoice was still in draft, never validated)
9. Go back to the Sales Order. It will be in the "Invoice Exception" state.
10. Click "Ignore Exception"

We like it because:

• The Delivery Order is a record of what was shipped.
• The Sales Order appears as completed in the list of sales orders.
• The canceled invoice shows the cost to the warranty.

It lacks a true journal accounting of the cost of the warranty. Since we don't use Journals, it's good enough for now.

I imagine an improved procedure would generate a true invoice and then reconcile it against a warranty journal.