An invoice is showing on reconciliation screen

I'd like to help you with your reconciliation concern, lkoups.

Transactions that will appear in the Reconcile page are the ones added from the Banking screen, or payment recorded to the bank account.

For the downloaded transaction, you'll want to go to the Banking page and undo it.

Here's how:

1. Go to Banking > Reviewed tab.
2. Search for the transaction and click the Undo link.

The transaction will be added back to the For Review section. Once done, open the Reconcile page and check if the invoice is removed.

With regard to the invoice recorded in QuickBooks, let's make sure that there's no payment linked to it by following these steps:

1. Click Sales > Customers.
2. Select the customer's name and open the invoice. If the invoice shows Paid, click the 1 payment made link.
3. Click the date to open the payment. Un-check the invoice to un-link the payment.
4. Hit the Save and close button.
5.  

If you see no payment on the invoice or the banking page it is worth going to chart of accounts and selecting the history for the bank account, you can then use the filter option to filter by amount (amongst other things)to find the payment.

I'm adding this article for more details: Reconcile an account in QuickBooks Online.

Please let me know how it goes by adding a reply on this thread. I'm just a few clicks away to help you some more. Take care.