Change in notice period & asking recovery aginst short notice per

I worked for a MNC company. As per my contract, notice period was 30 days ,but in between company has changed the notice period for 90 days. Company has send the notification through email.They have neither made any amendment in the contract nor taken any acceptance from me. In the month of october 2015 i resigned from the company .My reporting manager has accepted my resignation and asked me to serve notice period for 90 days. Then i told Hr and reporting manager that my notice period is 30 days and i shall serve the same.But they did not accepted it and then i escalated the matter to HR head through email . But he did not responded to the email as yet.I met several time to HR head and my department head but they insisted me to serve the notice period for 90 days.Finally they have released me on 45 th day. Now company is asking me to pay recovery against short notice period.Again I have sent same mail to company on notice period,Now hr executive has replied that..... "Mention may be made that in an employment contract, the employee is duty bound to adhere to the rules of the organisation in vogue. While accepting the employment the terms of employment were agreed by you unconditionally. In the circumstances, your present averments and contentions are purely an afterthought, especially in the light of the fact that the communication under reference was sent 8 months back. Hence the principle of estoppels would apply. Needless to mention that any further agitation on the subject matter would be resisted strongly and shall be construed as non-compliance of the rules of the company. This is without prejudice to our right to initiate legal actions, both civil & criminal for failure to comply with the terms of contract at your cost. Due to above issue company has not cleared my dues as yet. In such case, what should i do , should i go for legal recourse to get my dues clear? Thanks in advance for your opinions.