In order to remove the leave balances on an employee payslip, please try the following steps:
Repeat those steps for any types of leave that you wish to hide from the pay slips.
Changing that setting for Leave Categories should apply to pay slips, regardless of when the change was made. Deleting and re-creating the pay run should not refresh the settings for the other two employees.
In this instance, it would be advisable to reach out to us, so one of our support agents can assist you with this inquiry further: