It's nice to have in the Community. I'd be happy to help get this taken care of today.
When you emailed an invoice to your customer, and it's showing a paid status, it's possible that the Automatically apply credits in your settings is turned on. If the customer has an existing credit or overpayment, QuickBooks Online will automatically apply that credit to the newly created invoice.
Here's how you can check:
At the top right, click the Gear icon.
Select Account and Settings.
On the left pane, select Advanced.
Click on Automation.
If the Automatically apply credits box is marked, remove the check mark.