Admin can approve these late check-outs by navigating to Check-Ins – Check-Out section. From the drop-down list select the Pending Check-Outs and you will get the list of all the pending check outs. 
To approve individually click on the particular check out and roll down to Check Out Status. Select Approve or reject as per your requirement and click on the Refresh button to save it. 
Note: Once the status is saved you can’t change it.
Select the records and click on the Approve button to approve the check-outs.