Who financed the purchase of the flat? Is there evidence for this?
Under the Maharashtra Co-operative Societies Act, 1960 the first named person in the share certificate is called "Member" and the second and subsequent named persons are called Associate Members.
In your case you are the Member and your father is Associate Member. The question of Will will arise only if one of you die. If your father dies first (as we normally expect) his Associate Membership will get automatically extinguished and you will become the sole member with respect to the flat without any action on your part. You have only to submit the death certificate to the Society. Under the Act you can nominate person or persons to whom the flat should be transferred after your death. You can do this even now.
If your sister wants to make a claim on the property either after your father's death or after your death she will have to prove that your father had beneficiary rights in the property having partially or completely financed the purchase of the flat. Her success will depend on your answer to my first two questions.
Whatever may be the case by default the flat will come to you only and later to your nominees.
Nomination and Will have different connotations. A nomination doesn't transfer ownership. A nominee is only a trustee. But transfer of property to nominee is simple. The actual heirs to the property as per Will or under the Succession Act will have to claim it from the nominee. It can be an elaborate process. Further transfer by Will can require probate and a probate involves heavy stamp duty in Maharashtra.