Company is dishonouring the terms of employment

Hello, I used to work with a software company. I was on the verge of quitting my job, therefore I wrote various competitive exams and got through in one. It was a very crucial decision, I got the opportunity for higher studies in one of the prestigious institutions in India. Thus, I quit my job over it. As per the terms of employment, I have to either serve a 90 day notice period or pay up 3 month's salary. I opted for the latter. My HR refused to let me go without 3 months of service as was my manager. Therefore I resigned stating that I am ready to offer the 3 month's salary in lieu of the notice period and stopped going to office. As it would turn that I was marked absconded and a warning letter was issued in my name. It was told that I possessed the properties of the company and I was not supposed to hold those since I am no longer an employee of the company and the company can sue me if not returned. I immediately returned the belongings and informed immediately that I am ready for paying the receivable by the company from me. It so happened that the last working day was 7th October and I was dropping mails repeatedly before the date so that they would inform the amount payable for me to pay. It was informed to me on 23rd October that I had to pay a certain amount. the payment was realised by the company on 18th November. Recently I was issued the separation letter that I had not paid up in time. I am demanding a clean separation letter which recognises that I have no financial dues against the company or my money back as I have not erred in this case. Can I sue my employer?