Understanding the Management's Actions
While the action of the management is illegal, it is logical. They can't recover from your salary the PF deductions of the previous periods, nor will they be willing to pay it out of their pocket. So, they have taken the route of falsifying the joining dates, which is also an offense, but not likely to be actioned unless there is a complaint.
Deciding Your Course of Action
Your approach should depend on what you want to do and your career choices. If you want to remain in this company, then don't do anything. Accept the fact that at least now you are getting the PF.
If you wish, you or any other employee can approach the PF Office and meet the PRO, vigilance, or even the Deputy Commissioner to file a complaint. For that, you need proof that you were working there for more than a year. Perhaps you need to show them your appointment letter and previous salary slips.
Potential Consequences
But remember that if you do so, you are likely to soon lose your job because your company will easily identify that you went and complained, and they will find some excuses to remove you. It is also possible that the inspector who comes to check will accept a bribe and put a report showing evidence that your complaint is false. While there are tools like RTI and social media today which make them cautious in dealing with such cases, it's a long-haul battle in the Indian context.
So make your choices and act accordingly.