You're on the right track with reconciling your master account solely in QuickBooks Online (QBO), GrayCat99. Let's explore this topic further to address the imbalance.

When it's time to reconcile your QBO accounts, focus only on the parent account. This is because all transactions from the associated sub-accounts are automatically included in the total balance of the parent account.

Furthermore, to resolve duplicate transactions after merging your accounts, pull up the bank statements and compare them with your bank register. This process will help ensure that no transactions are duplicated or missing from your combined account.

Upon doing so, it would be best to contact your accountant to assist you while comparing your bank statement and bank register.

Additionally, QBO automatically provides a reconciliation report each time you complete a reconciliation. This report is helpful if you encounter difficulties reconciling the subsequent month, as well as when you consult with your accountant.

Consistency and accuracy are crucial for effective financial management. Tag my name in the comments below for any follow-up questions or concerns regarding your QBO accounts. I'm just a notification bell away.