Uncommon Payroll Deduction

SUGGESTED

I have an employee that was issued a payroll check back in 11/2014, and it was lost.  The owner decided not to stop payment and reissue, she just had me reissue another payroll check.  Understandably, this employee is the most trustworthy individual on the planet.  Well, BOTH checks cleared recently.  How do I go about deducting from the employees next payroll check the amount owed back to the company?