I deleted a payment that was a duplicate after it had been reconciled. Now the transaction is being flagged on my reconciliation report. How do I correct this?

Hello there, @usertcuster63. 
 

Let me clarify a few things and I will help you correct your reconciliation discrepancy.
 

The Reconciliation report will contain all of the transactions that you reconciled (including the duplicates). The Reconciliation Discrepancy report will immediately update whenever one of them is deleted (regardless of whether it is a duplicate).

We can recreate the transaction by checking the details in the audit log and manually mark (R) in the chart of accounts.
 

Here's how: 
 

1. Go to the Gear icon and select Audit Log.
2. Look for the deleted transaction and click View.
3. Click the arrow on when it was created and deleted.
4. Take note of the transaction details.
5. Recreate the transaction manually by clicking the Create menu.
    

After we recreate the transaction, we can go back to your register and change its status to Reconciled (R) manually.
 

I'd also suggest you check your bank statement to compare the transaction in the register. If it's really a duplicate, it is possible that there's an incorrect transaction that needs to be deleted or recreated.
 

For further information about reconciliation, see the following articles:
 

• Undo and remove transactions from reconciliations in QuickBooks Online.
• Reconcile an account in QuickBooks Online.
• Undo your client’s reconciliations with QuickBooks Online Accountant.
   

Don't hesitate to get back if you have any other concerns or a hard time navigating the other features in QuickBooks Online. I'll be happy to help you out. Have a great day!