Thanks for reaching out to us, anastasiav.
I'll know how to reconcile non-reconciled transactions without affecting the current reconciliation balance.
Since you still have the correct balance on your current reconciliation, there might be an adjustment entry created while reconciling the affected period. To fix this, let's review the affected period reconciliation report. I'll show you how.
- Go to Accounting on the left menu.
- Select Reconcile tab.
- Click Summary in the upper-right corner.

- Choose the reconciliation report of the affected period.
- In the reconciliation report, look for Adjustment and make sure the amount is the same as the non-reconciled transaction.
You can delete the Adjustment in the reconciliation report if the amount is the same as the non-reconciled transaction.
Here's how:
- Go back to the reconciliation report and click the amount associated with the Adjustment.
- This will open a transaction window. Select More at the bottom.
- Choose Delete, then Yes to confirm the action.
After that, you can manually reconcile any unreconciled transactions in your bank register.
Here's how:
- Click Accounting on the left menu and go to the Chart of Accounts tab.
- Look for the affected account and click View register.
- Look for the non-reconciled transaction and change the transaction status from blank or Cleared (C) to Reconciled (R).
- Click Save, then Yes to confirm the action.
I've also included this article for future reference in case you need to undo or remove transactions from reconciliation: Undo or remove transactions from reconciliations in QuickBooks Online.
I'm always here to assist you in managing your QuickBooks transactions, just leave a comment below. Have a great day.