TDS on salary not deducted

One of our clients has received Intimation under section 200A of the Income Tax Act, 1961 regarding short deduction of Tax on Salary paid to one of his employee under Section 192. However the amount of short deduction was paid by the employee on self assessment while submitting his own Return of Income. Our client have intimated the ITO TDS that the amount of short deduction has already been paid by the employee and so the amount of short deduction cannot be demanded from them and also submitted a copy of the tax paid challan along with the copy of IT Acknowledgment of his employee with the ITO TDS. However the ITO TDS have rejected the plea of the client and asked him to revise the e-TDS Return. Please let us know how the concerned return will be revised considering the facts of the case and : 1) Since the amount of short deduction has been paid by the employee under his own PAN the same cannot be incorporated in the revised return to be filed. 2) If the amount is now collected from the employee and deposited in the Government Account and then revised e-TDS return is filed, the employee shall be burdened with double taxation as he cannot file his own revise Return of Income as the Original Return was filed after the due date.