Rights of nominee to fixeddeposits

It is correct that the nominee is only the caretaker of the FDs and not the owner or beneficiary.

Since the Immovable assets were not mentioned in the Will they will be divided as per the Hindu Succession Act. In this case, the first degree relatives (children, parents, spouse) of the deceased will have equal share in the FDs. If there are no first degree relatives, then second degree relatives (brothers, sisters, etc.) will have equal share.

In this case, since the movable assets are willed to the brother's daughter, the court may also infer that the FDs were also bequeathed to her (constructive interpretation). If she has filed for probate of the will, then I suggest that you challenge the same in court.