There's a revenue guide to what to do. It's explained in section 5
here. The employee repays the net amount and the employer does a payroll entry with negative pay and negative tax to balance everything.
BTW Brendan's solution further up would result in revenue footing the bill for the employee's undue bonus which, apart from that not making sense, would be flagged by the paye system as the gross pay and tax figures wouldn't tally with the employee's tax credits.