Hello Victoria,
When you reconciled the transactions (including the duplicates), they will all be part of the Reconciliation report. Deleting one of them (regardless if this is a duplicate) will automatically reflect on the Reconciliation Discrepancy report.
There are two ways to undo the whole reconciliation. This will remove the history of the deleted duplicates.
If you choose to invite your accountant, they'll have an option to undo the reconciled period at once. You can share this article for them to know how: Undo your client’s reconciliations with QuickBooks Online Accountant.
If you want to undo the reconciled transactions yourself, you can follow Step 2 in this article for the detailed instructions: Undo and remove transactions from reconciliations in QuickBooks Online.
After undoing the reconciled transactions, you can reconcile the period again. You don't need to worry about the duplicates since you've mentioned earlier that you've already deleted them.
To know more about the reconciliation, you can browse this article: Learn the reconcile workflow in QuickBooks.
We'll be right here if you require our assistance in correcting your reconciliation. Have a great day!
