When creating an invoice as a claim that can be rejected and the amount/percentage changed. This is true for both Prime and Sub Invoices.
Idea would be to add a new Claimed column where the existing columns would be used as the certified amounts. Plus add a notes field where you can record the reason why the claimed and certified amounts are different.
So you would produce the "Claim" and the claimed and certified would initially match. If you then got the certified amount from Customer (Prime Invoice) or you were certifying a Subcontractor (Sub Invoice) and you changed the certified amount the claimed amount wouldn't change and you could record notes why the customer is certifying less or why you are not certifying the Subcontractor for the full amount.
This would then need to be added to doc templates especially for Sub Invoice payment certification where you can present back to Subcontractor what they claimed vs what you certified and reasons why