Notice period increased from 30 day to 90 without consent

As per your situation, I must tell you that you are not obligated to undertake the updated 90-day notice period, considering that your appointment letter would be having the clause of 30-day notice period and since this appointment letter is binding upon you and the organization, you are obligated to serve only the 30-day period.  

Nowadays, various companies put a variation clause in their employment contracts, which gives them the power to bring changes in the contract if and when they want. But it should be noted here that such a change in the contract needs to be properly communicated to the employees, and their acceptance should be sought before such updated provisions become binding upon them. In the present case, though the company communicated the change to the employees on 25^th June, the same was not accepted by you, therefore, the updated terms won’t be applicable to you, since the communication of acceptance was not completed and hence no agreement was made. Consequently, no contract came into being. So you can be relieved on 30^th June and the company is obligated to give you the relieving letter.