I appreciate you for sharing your concern here in the Community, chris-errcsdesig.

I'm here to help you remove duplicates and link invoices to QB payments in QuickBooks Online (QBO).

First, we'll delete the manually created deposit and then undo the one from your banking.

Here’s how to delete:
 

1. Go to the Accounting menu and choose Chart of Accounts.
2. Locate and click the View register of your bank.
3. Click the manually created Deposit and select Delete.
4. Hit OK to confirm.
    

Undo the added Deposit from the Banking page:
 

1. From the Banking menu, tap the bank where the deposit came from.
2. Choose the Reviewed tab, and look for the deposit.
3. Click Undo under the ACTION column.

After deleting or resetting the deposits, we’ll match the invoice that was already paid to the cleared deposit from the Banking page.
 

1. Still from the Banking page, tick the bank and look for the deposit in For Review.
2. Click the deposit and select Find match.
3. Filter the Date range that includes the date when the invoice payment was created.
4. Check the Payment and then click Save.
    

Once done, try to run the Profit &Loss report again to check if the total is correct.

For future help, here are some links that cover all the details on how to perform the following tasks in QBO.
 

• Record a customer refund in QuickBooks Online
• Handle a customer credit or overpayment in QuickBooks Online
   

Come can visit us again if you have other questions about managing invoices. I'd be more than happy to help. Have a great day!