I see this is your first post so I'd like to welcome you to the Community, Gator1,
I can help you correct your reconciled deposits in QuickBooks Desktop.
You're on the right track with deleting those duplicate transactions. Once removed, you can now add the right deposit to the invoice using the Receive Payments option to prevent it from being open or unpaid. Let me show you how to do that:
- Open the invoice.
- At the top section of the transaction, click on Receive Payments.
- On the Customer Payment window, select the correct deposit.
- Click Save & Close.
Check out this article to know more about recording invoice payments in QuickBooks Desktop: Record a Payment for an Invoice
After you modify a reconciled transaction it automatically gets unreconciled, so you'll need to run a mini-reconciliation to save the changes in your bank register. You may refer to this article for the complete steps: Reconcile Previously Deleted and Re-entered Checking or Credit Card Transactions
That should point you in the right direction, Gator1. Please get back to me if you need further assistance with QuickBooks. You got me here to figure things out for you. Have a great day!