Many times I hear QuickBooks users say the beginning balance in the bank reconciliation window is wrong and they do not know how to fix it. If a transaction has been voided, deleted and re-entered or otherwise un-reconciled, it will affect the beginning balance in the reconciliation window. You should never just mark transactions as cleared in the register, since they will still show in the reconciliation window. To clear and reconcile them and fix the beginning balance in the reconciliation window (and re set the date if needed), it is necessary to reconcile the account again.
For example, if payroll taxes (or Sales Taxes) were paid with a regular check instead of via the Pay Liabilities window, it is necessary to delete the check and replace it with a Tax Payment. If the check was previously cleared, this will change the beginning balance in the reconciliation window. Thus, it is necessary to reconcile again and mark the corrcted tax payment as cleared.
Enter the last statement ending date (or one day different to preserve the original reconciliation report) and ending balance (but not any service charge or interest), reconcile the account again marking the changed transactions as cleared. The difference should be zero. This will fix the beginning balance and reconciliation date.