I have an odd question that I have never run into before. In 2019 an employee that owns 100% of a company had EI deductions coming off of their payroll. Their accountant has asked to have their T4 amended to show that there were no EI deductions because they are ineligible and should not be paying into it. It has been updated for 2020 but should their T4 be amended to show the amount paid into EI was actually income tax instead? This makes me a bit hesitant to amend a T4 that has already been processed and sent to CRA but I don't have much tax experience. 

Would the employee not just check off that they are ineligible for EI when filing their personal taxes for 2019 and CRA would allocated the deduction accordingly?