If we understand this correctly, your friend absconded, and thereafter the company terminated him. However, they updated the records in PF after 3 months. Obviously, they wouldn't do it with retrospective effect and face a penalty, so they used the current date. The intervening period is an NCP. Obviously again, he joined the other company without completing the notice period or formalities from the previous company.
There is no way to rectify the overlap. At best, he can go and explain it to the HR, specifically showing that no PF contribution happened during those 3 months.