To remove a line item from an invoice (in the event of a duplicate or incorrect entry, etc.),  you need to delete to the original entry on the Work page. In this example, the contractor has 6 deliveries when the correct amount should be 3.

Since everything added through the Work dashboard creates a payable entry under Payments, the Work dashboard acts as the “source of truth” for payable invoices. Deleting the Work Entry for the duplicate Deliveries will automatically correct the invoice:

After deleting the duplicate work entry in the Work tab, the payment is automatically recalculated and is now correct: