I can show you other troubleshooting steps, 

QuickBooks will only recognize an estimate as closed if you've linked it to an invoice. If you want to get rid of these transactions, we'll have close or delete them. Since these are non-posting transactions, eliminating them won't affect your books. 

Looks like the same thing happens even after linking them to an invoice and running the verify and rebuild process. We can update QuickBooks Desktop to the latest release and then run and install the QuickBooks Tool Hub to help fix company data damage.

Check out this article that will guide you in splitting an estimate into as many invoices as you need: Set up and send progress invoices in QuickBooks Desktop. It also contains information that will help you track how much you invoice for each estimate.

Don't hesitate to visit us again with all of your QuickBooks-related concerns and questions. The Community is always here to help you succeed.