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.
- Go to Employees tab.
- Select the name of the employee.
- Select Opening Balances from the left-hand menu
- 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!