Let me share some information when deleting a duplicate payroll deduction in QuickBooks Online.
While you can remove a deduction in the Employee's setup, it will remain in the deduction list if the deduction was used before. Since you can't fully remove it from the list, you can edit the deduction name as not in use or make up your description.
In your QuickBooks Online account, select Workers. Then, click Employees.
Select the name of the employee. Under Employee details, choose the edit (pencil) icon beside Pay.
Select the edit (pencil) icon next to the deduction item.
Select the trash bin icon beside the deduction item. Then select Yes to confirm the deletion.