I'm glad to hear you caught the double entry. Noticing these things early on goes a long way in making sure your books balance, and reconciling is a great way to identify missing or duplicate transactions. As soon as a transaction is record in QuickBooks Online, it affects your general ledger (even if it's never marked as reconciled). If you noticed a duplicate transaction while reconciling, it will continue to affect your books until it's voided or deleted.
You can easily open the transaction directly from the ledger or reconciliation screen. Here's a handy article explaining how to address a transaction that needs to be removed from your books: Void or delete transactions in QuickBooks Online
Feel free to reach out if you'd like any more help.