There is a dashboard that will show Employees that are still active in Past Jobs.  

Once you have that list, you will need to run a Conversion Workbench to run the proper utility.

This screen is the admin entry to the menu items above.  

The utility you need to run is is User Run Conversions -> 630 / 660 (End Activity on Active Labor Transactions Process / End Activity on Labor Header Transactions Process)

Click the checkboxes next to both of the processes, then go to Actions -> Run Pending Conversions

I finally found a method to surface this utility on the menu system, so it can also be reached by running the 2 items below.

Most of the work will be with the Detail Transactions.  Enter the employee number ofr the first employee needed ito be clocked out, tab, then click the Get Detail Transactions button.  Check any transaction where the clock in date is before today, then Submit the process,  It will take a few minutes to clock out each employee form the job.  Repeat for all other employees

Repeat the process for the Header transactions.  Do nothing if the Clock In Date is today, otherwise check the record, then submit.