Jason,
Have you tried your test with a deposit invoice instead of Advance Billing? The advanced billing is specific to the line, whereas the deposit invoice is against a total sales order.
The issue I would see with changing the line to the full 11,700 in your case would be if that misc. charge should be going to a different GL than the product group (e.g. engineering fee or expediting rather than product sales).
I like the flexibility of deposit invoices compared to advanced billing. If an order line changes after having an advanced billing against it there can be more work than if you just use a deposit invoice at the order level.
Jenn