Hi Akshat
You can use same PC00_M40_CMAP transaction to unmap challan for a single employee.
1st Step Enter Payroll Area Payroll Period
2nd Step Enter TAN Number
3rd Step Select Challan No.
4th Step Further Processing > Enter
Company Code
Personnel Area
Personnel Number
Next Screen , Use reverse arrow button (Remove mapping of selected Rec) to unmap the challan mapping.
Click on Review and Save.
Try this in your test system first.
Regards
Chetan Bajaj