Hi Jackies2,

Thanks for posting in the Community!

Whatever the supposed annual leave balance they have, you can enter it as an opening balance on your employee's profile before you process a final pay. If they are currently showing a negative amount on the employee Leave Balances page, you can simply add the value of those negative amounts to the Opening Balances section for the annual leave category - this will cancel out the amounts and leave them with nil balances under each of the leave categories that were paid out. 

1. Go to Employees tab.
2. Select the name of the employee.
3. Select Opening Balances from the left-hand menu
4. Select the Leave Balances tab and enter the amounts to balance out the leave accruals, then select Save.

For your reference, you can check on this article: Terminating an Employee. 

Feel free to drop a comment below if you need further assistance. Have a great day!