Thanks for the clarification.
Two points you have not responsed to - one about number of contract workers and second about the supervisor / visit of the contractor.
Please check the above two aspects also, the purpose is to know if there were sufficient number of contract labour requiring RC by the PE and license by the Contractor, and whether same was done or not. The purpose of checking supervisor / visit of the contractor is to establish the supervision and control over the contract workers deployed at your premises.
The Relief is possible to the said contract worker only if he is able to establish that the contract was Sham and there was direct master servant relationship between the PE and the said contract Worker. Supreme Court in the case of "Ram Singh Vs Union Territory, Chandigarh, Haldia Refinery Canteen Employees Union Vs IOC, International Airport Authority of India Vs International Air Cargo Workers Union etc has amply clarified this.
Whats needs to be seen / checked is:
1. Who has supervision and control?
2.Who does the selection and Rejection of the workers to be engaged?
3. Who pays remuniration?
4.Who deduct Insurance contribution ?
5. Who organises the work ?
6. Who supplies tools and material for work ?
7.Who sanctions leaves / advances / loans etc
8. Whether there is valid agreement ?
9. Whether the contractor has issued appointment letter ? etc.. etc..
Thus, just one proof with the contract worker will not establish that he was your employee, if you are able to establish other facts.
However, the service certificate issued by you and the fact that Contractor has not retrenched the worker may go against you. If it is recent case ( 1 -2 months ), you can ask the contractor to formally terminate their service and retrench him legally by making the application and also paying him retrenchment compensation and notice pay under section 25 F of the ID Act - all this has to be done by the contractor, you can reimburse the expenses.. This will strengthen your case if rest of the things are in place.
You are right, contract worker will never seek reinstatement with the contractor, he will always raise dispute agansit the copmany, because he knows that he can not get any thing from the contractor.