If you'll pay him again, add the money to the paycheck using the 401k item (backwards), or if that is not allowed, set up an addition item and code it to the 401k tax tracking type.
If not, then enter an employee-based liability adjustment for the 401k amount. On the adjustment Click the Accounts Affected button and pick Do not affect accounts. This will impact payroll reporting but not your accounting.
Then write him a standard check using the same liability account the 401k item uses to back out the accounting.
