Best practice to do balance adjustments for grossed-up imputed earnings when employee tax not report

We had created an imputed earnings element for gift cards given to employees and also grossed it up. We did not realize that the employee taxes were not reported on the periodic tax report. We have fixed that issue, but we need to do balance adjustments so the correct taxes are reported and paid for the employees. We are not getting the results we expect with the balance adjustments. For example, the run results have the same amount in Medicare Employee Tax and Medicare Employee Tax Not Taken. What is the best approach to fix