Is the registration of an agreement to transfer a flat necessary after the registration of a co-operative society?

No. After registration of a co-operative society the purchasers of various premises become members and shareholders of such a society, and as such the members are thereby governed under the provisions of The Maharashtra Co-operative Societies Act, 1960.
Under Section 41 of the Maharashtra Co-Operative societies Act, 1960, the provisions of clause (b) and (c) of sub section (1) of Section 17 of the Registration Act, 1908 do not apply to any instrument relating to shares in a society although the assets of the society consist in whole or in part of immovable property.
In a registered society, the member actually transfers his right in the shares held by him and consequently transfers the premises in his use, occupation and possession. Thus, it is not necessary to register such an agreement.