Harassment in public sector bank after submitting resignation application

I joined a government bank in 2019 as a probationary officer and in the year 2022 I decided to resign as I wanted to pursue higher studies. A day after I applied for resignation, I was sent an explanation letter through email from the Zonal Office seeking my explanation regarding irregularities in loan accounts in which I had absolutely no involvement in. Interestingly, the date mentioned in the letter was prior to my resignation. I was handling the operations department exclusively being a probationary officer and the manager was handling the loan department. I submitted my resignation mentioning all the facts and how according to the CVC guidelines, a probationary officer should not be posted in a single officer branch as a second officer. I was posted there as a second officer which is a clear violation of the guidelines. I mentioned how a probationary officer can't be asked to process and recommend loans and how I didn't sign anywhere in any loan document. But, the head of the office in an attempt to delay the process said he wasn't convinced with my explanation and forwarded it to the vigilance department. Just three days to go before the end of my notice period of 3 months, I received an email from the HR department saying that my application has been declined due to pending departmental proceedings. An insider told me that it was deliberately sent to the vigilance department out of vindictiveness. I could somehow manage to get in touch with the vigilance department and told them how I was neither the appraising nor the sanctioning authority of loans and how I was being harassed out of vindictiveness. I have been assured that I will get the clearance soon. However, the Hr told me that I again have to apply for my resignation and then serve for 3 more months or give 3 months of salary. Now, how is it right on their part to ask me to serve for three more months when I have already complete 3 months of notice period ? It was their responsibility to complete all the formalities within 3 months and then relieve me. Why will I suffer because of their laziness and vindictiveness ? It is very clear that they knew that if they forwarded this to vigilance, it would delay things and that is exactly what they did. Please advice me as to what I should do and whom I should approach to make sure I would not have to serve for another 3 months. My resignation letter clearly stated that I shall relinquish office on the expiry of 3 months from the date I gave my resignation.