Hi Gina60 - thanks for your question.
It's easy to adjust an employee's annual leave balance - exactly the way you thought: just do it in a pay run. Simply change the annual leave accrual amount in the pay to increase or decrease their leave balance.
For example, if you need to reduce the employee's leave balance, simply enter a negative value in the leave accrual field in the pay run.
You can do this in the employee's next pay, or you can fix it in a separate adjustment pay - here are the instructions.
I hope this helps!
Adrian