"The Limitation Act" does not apply to ESI and EPF. Factory records should be preserved for at least 3 years. Now, since most of the records are maintained online, soft copies of records should be downloaded and preserved on the hard drive.
You need to have a Record Retention Policy framed complying with all legal requirements since the period of limitation varies from Act to Act, and in many cases, there is none, as in the Factories Act. Much knowledge on the matter is available in the search option of Citehr. Once you have developed the policy, you will be able to defend the matter properly.
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