This article explains how to make fee adjustments against an invoice.
Creating a Fee Adjustment
Go to create an invoice - adjust the Fees or Disbursement to reflect the change you would like to make, a box will appear asking if you would like to show as a discount or hide line pricing and show total only. When choosing "hide line pricing and how total only" we are adding a fee adjustment to the invoice and this adjustment will not appear on the invoice that you send to the client.
Depending on your invoice template a fee adjustment will not show on the invoice.