If the discrepancy is noticed as a shortfall, naturally, they will initiate an enquiry and send you a notice under Section 7A of the EPF & MP Act. When the establishment has found discrepancies, they should also be given an opportunity, right?
Therefore, you have to write to the PF Enforcement Officer/Asst PF Commissioner and seek permission to address the issue in a personal hearing. You can also directly meet the Accounts Officer with this letter to reconcile the payments and fix it. Please note that the EPFO's offices treat the employers and the members very poorly nowadays, and there will be many hurdles before you can get an opportunity to meet an officer. But since the issue is important to us, we need to compromise a lot.