1) you have to reply to the notice
2) mention that you had submitted resignation
3) the company for reasons best known did not reply rejecting the resignation letter
4) you have duly servrd the 90days notice period
5) the company is deemed th have accepted the resignation letter
6) only after you discontinued job did company say resignation cannot be accepted
7) the chargesheet that you are unauthorisedly absent is unsustainable in law
8) contact a local lawyer