Management doing domestic enquiry

The issue involved is "whether there was a treachery, by stealing data from employer" and it was later misused. You have not informed the name of the company whether PSU or private.  The burden of establishing the theft rests on management.  Do not presume things, as a technocrat, you are aware of the facts and technology involved to find out about data theft.  Generally, no employer takes such a serious step of filing cases against any employee as their focus is on the management.  It appears that they have concrete evidence with them for taking an extreme step against an officer.  If everything goes smoothly, accepting the resignation and deducting one month's salary is a simple thing, and getting a substitute is not a difficult thing, , but in your specific case, they are spending huge amounts and engaged in further activities that involve wastage of time and money.  In this case, you have filed a case for recovery from the employer, provocating them and complicating the issue, as they have forgotten your misdemeanor if any.

You have to deny the charges in the inquiry and proceed further when they refuse to 

Consult and engage a local prudent lawyer practicing service matters for proper analyses of facts, professional advise and necessary proceeding.

No domestic enquiry/procedure is legally permissible once the employer-employee has ceased. 

what waqs the agreement providing for notice period on resignation.