I desperately want to understand what you're saying to do but everything I've done to follow what I think you're saying does nothing to fix my problem  The invoice will look right and the accounting looks right but when I create the next invoice it shows I'm overbilled more.  

I have an estimate that had a deductive change order.  I'm overbilled on a couple line items at 100.14%.  Doing everything as I understand it still creates the next invoice as overbilled at 100.28% and screws the prior billing amounts up.  

Please help!