Adjustment to taxable income for a terminated employee

Good morning.  We have a situation where we have failed a "non-discrimination" test for Highly Compensated Employees for Flexible Spending Dependent Care, and the employee has since resigned from the Company.  We have been told that we have to increase his taxable income by a certain amount (let's just say it is $1,000), and I'm assuming as part of this we need to decrease the amount of Dependent Care Flexible Spending that is attributed to this employee (for W-2 reporting purposes).  Is there a way to process a check in order to accomplish this?