I have a main CC and employee cards under it. To reconcile them I was downloading the transactions to the main. An ex employee put each employee card separated. Is a mess

Glad to see you here in the Community, @bluehammerllc. Allow me to share my thoughts on your concern about duplicate transactions recorded in your bank account.

To isolate this issue, you can remove those double transactions by deleting them manually.

Here's how:

1. Open the transaction.
2. Then select Delete.
3. Hit Yes to confirm the action.
4. Repeat the steps for other transactions.

 
In addition I’ve got this helpful article to guide you further on how to add transactions if with parent subaccount and reconcile them in QuickBooks Online.

Also, I’ll share with you these articles to help you fix issues you’ve encountered when reconciling.

• Fix Issues At End Of A Reconciliation In QuickBooks Online.
• Fix Issues The First Time You Reconcile An Account in QuickBooks Online.
• Fix Issues for Accounts You’ve Reconciled in the Past in QuickBooks Online.

 
Feel free to reach out if you have any further questions about reconciliation in QuickBooks Online. Have a good one!