Proration of No Pay Leave is not based on Modify Leave in the Leave module, but it is based on the Leave deduction that you have processed in the Payroll. You may need to reprocess your pay records of the prior months to reflect the leave deduction correctly in the payroll.
Please check as follows to check the incorrect proration of the no-pay leave for your bonus:
Go to the Payroll module.
Click Reports and select Pay Records Report.
Select Leave Deduction Record Report.
Select the Year and Month from 1 to 12 and select NPL only.