Transfer Fee to Society in case of Merger of Corporate

In our Society Bank A had 42 flats (individual agreement) out of total 105 flats. They use it as their Staff Quarter. Bank A later on was taken over by Bank B with RBI's approval. Bank B approached us to transfer the said flats in their name. As per By-Laws we demanded Bank B to pay Rs.25,000/- per flat as Transfer fee. Bank B was reluctant to pay the sum saying it was not a sale-purchase agreement and they got the property by virtue of Merger approved by RBI. They later arranged an Opinion from someone to claim their Point. We too took opinion from a Property Lawyer who opined that (1) By-Laws specifically mention where Transfer Fee is not payable and merger is not one of them (2) The deed of merger does not speak anywhere that Bank B need not have to pay Transfer fee and (3) RBI Act does not supersede Bombay Co-operative Society Act, hence Bank B is liable to pay Transfer Fee. Its more than 3 years now and when we started following-up with them, they are threatening us to file case against the society. We are hesitating to transfer because tomorrow anyone can accuse us for doing wrong in connivance with Bank B. Kindly suggest what should be done as going to court will be expensive for us.