Can wife file a divorce after deserting husband and living separately for 2 years

The outcome depends on the facts and pleadings.  Mutual divorce.  in the family court is a better option.  There should be a specific reason as stated in the Act for seeking a divorce, and perhaps your local advocate may invent such reasons that favor you.

The woman has to get hold of a good lawyer who will cook up a story as follows: The husband has deserted the woman for two years under section 13 of Hindu Marriage Act and arrange evidence accordingly. The prosecution has to establish that the husband has not provided her with maintainance for past two years. There is seperation of bedding and boarding.Thus, there is a possibility that judge may get convinced and give judgement in favour of the woman. The defence: The respondent(husband) can file a petition of ROCR(Section 9 of Hindu Marriage Act) and claim his whole property back(through a petition), if the divorce is evident.