When processing the pay run, you will see a notification icon on the View timesheet button. This will remain until you edit the payment in Payroll. You must remove the deleted payment category and replace it with a new one if needed.  
Clicking the View timesheet button will open the side panel, which will give more details about what has been deleted.  
NOTE: This will not retrospectively change any payrolls you have already processed.
You can then click on the Manage payments heading, or browse to: - Settings in the menu bar.
- Under the Pay run heading choose Payments and deductions.
- Identify the relevant payment and click Edit.
- Under HR timesheet category, click the X next to the category that has been deleted from HR.
- If necessary, choose another category from the list.
- Click Save
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