No problem, Sathish. You can upload the contribution using his old P.F. number. I have done it many times.
Recently, we attended a meeting in Dindigul, conducted by the A.C. of P.F. We raised the same question to him. He clearly told us, "No problem, you can give the same number." He also said, "If an employee has not settled his account, you can give the same number."
If someone does not come to work for three months, you have to mention that the periods are a break in the service period during his settlement time.