Thanks for reaching out to us. Let me assist you with your invoices.
If you'll delete a paid invoice, it'll result in unapplied cash payment and this could be the reason why the balance is incorrect. You also want to delete the payment since you only mark the invoice as paid by error. Follow these steps:
Go to the Sales menu and select Customers.
Click the customer's name and locate the payment transaction.
From the Action column, click the drop-down and select Delete.
Tap Yes to confirm.
Here are some of the articles you can check. These will explain more on how to handle unapplied cash and bill payments in QuickBooks Online: