We are a small audio video and electrical contracting company and have the same issue.  When I add change orders to an existing estimate that already has invoicing against it, the Change order imported to the existing estimate breaks the previous invoicing links.  I have to import the change order to the estimate, delete any past invoices (record the date, inv #, and amount) and then recreate the progress from the beginning just to be able to create a new progressive invoice with the correct new amount due.   The existing links in progressive invoicing should not be broken when needing to add to an existing estimate!!!!!!