I am not saying that you did this mistake.
As I already mentioned above, in my views you should remove the new number of such employees and get enroll their old number under your employer code and do the compliance in that old number for future. For future reference, you should keep the current contribution history. So that, if any inspection comes in future, you can show the same.
Please do not worry about this mistake. Just go online site of ESIC login in your ESIC Portal & Enrolled them again providing with old ESIC Insurance Number. Get printout of enrolled Form & verify by putting Stamp & Signature by the authorized person of your organization and give to related insured person. Copy of this enrolment Form may be show at the time when they need medical assistance from ESUIC dispensary.
At the time of ESIC contribution uploading, please show name & ESIC Number (New Number allotted by mistake) of Persons a showing 0 wages and code 0.