In the books of the Co-operative Society when A was alive B would have been Member of the Society and A, Associate Member. If A dies, as B is already a member the flat, B will automatically become the sole member of the flat. Under the co-operative law in Maharashtra an Associate Member need not necessarily be beneficial owner of the flat. There is provision in the law only for the first member to make nomination. There is no provision for an Associate Member to give nomination.
Section 30 of the co-operative societies act gives right to give nomination only to the first member of the Society and not for other members. If others had beneficial interest in the property, they should make a will. In the Will he or she should first state how they had benefitial interest and what percentage and how they have right to bequeth it.
Whom had A wanted to nominate? Has the nomination been signed by witnesses? How many witnesses and who are the witnesses? Have A and B got children? How old are they? Who are the living natural heirs of A?
If there was no problem B can continue as member with the flat under his or her sole name. Specifically if you answer all the above questions, I can give suitable reply or suggestions.