Wait. you have no guarantee the IRS will see things your way. I assume you filed as an IC. as such you may have taken certain page 1 deductions including the QBI deduction (line 13 of 1040). As an employee, those deductions are not allowed but you will get back the SE tax you paid. however, I don't know if your employer can come after you for your share of the FICA and Medicare taxes that would have been taken out of your paycheck as an employee. you also can't be sure of what numbers will be on the W-2 that the employer will need to issue to you.