Processing adjustment for overpaid employee who wrote a check to the organization.

An employee was mistakenly paid a sign-on bonus this year and has written a check to the organization for the net overpayment amount.

The sign-on bonus is a supplemental payment and creates separate entries/calculation but is included in the Calculate Payroll and Calculate Prepayments for the period and paid with regular earnings. That being the case, I am not able to reverse the calculate payroll for just the bonus portion.

How would your organization make the corrections to reduce the YTD wages, taxes and 403b balances? Looking for best practices and suggestions.