Welcome to the Community space, @accounts-madhatg. I appreciate you providing detailed information about the problem you encountered on your invoices. 

I checked my resources and haven't find any reports about the number not adding correctly on invoice when lines are removed. 

Have you tried basic troubleshooting, such as logging out of the account and signing back in to link an estimate or time charge? If you have, let’s make sure the issue isn’t browser related by loading the site using a different browser or a private window.

Here's how:

• Press the Ctrl + Shift + N (Google Chrome) keys on your keyboard.
• Press the Ctrl + Shift + P (Firefox or Internet Explorer) keys on your keyboard.
• Press Control + Option + P (Safari) keys on your keyboard.

After that, try to check if everything is good. If yes, go back to your default browser and clear cache. See Clear cache and cookies to fix issues when using QuickBooks Online for more information.

You can also send screenshots here in the Community, but make sure to black out sensitive information to protect the account. This is for me to get a better picture of what's happening and ensure we are on the same page.

For your future reference, here's an article if you need to receive partial invoice payment from your customer: Record invoice payments in QuickBooks Online. 

Our doors are always open to help you again if you have any other concerns or follow-up questions about creating invoices. I'll be around to provide further assistance.