It is a very rare scenario when the balances in the two panes of Bank Acc. Reconciliation window match. During the course of the reconciliation period, there would have been adjustments, errors, and other reasons leading to a mismatch.
While the auto reconcile reduces the time and effort to reconcile most of the entries, the investigation of the unreconciled line items is still a manual process.
When a particular transaction is not reflecting in the bank statement, it may be an entry that was passed in NAV by mistake and needs to be reversed. If the transaction did occur, you can get clarification from the bank.
If there is an entry in the bank statement and the corresponding line item is missing in NAV, you can just create a new entry.
In some cases, you will find the entries in both the panes with a mismatch in the amount. Or you may find that the amount is matching but the ‘client name’ is different. In such cases, you have to manually check why there is a discrepancy and make corrections based on your findings.