Percent (%) Complete value is brought from the Projects screen. It is stored in the invoice record when processed via the Batch Invoice method and can be displayed on the invoices. When creating batch invoices, you can enter or update the % Complete field and the Net Bill is calculated accordingly. % Complete first calculates the % of the total contract less previously billed services and then adds the project-level tax percentage on top for the current service amount that you are trying to bill. Using this option, Core automatically calculates your pre-tax amount and adds the tax (HST). When you apply % Complete, Core writes up or writes down (WUD) the value of time entries automatically.
You can also do Percent Complete billing in another way. Please check the help file for more here.