Pagdi system flats are governed by the Maharashtra Rent Control Act, 1999.
The tenant does not own the flat – ownership remains with the landlord.
The tenant only has tenancy rights, though those rights are heritable.
On death of a tenant, tenancy rights devolve upon certain family members residing with him at the time of death (spouse, children, etc.), under Section 7(15)(d) of the Act.
If only your maternal uncle continued living there, he may have become the de facto tenant in practice, but legally the rights did not automatically extinguish the rights of your mother (his sister).
If rent receipts were never transferred to his name, and your mother’s consent was not taken, the legality of his “exclusive” redevelopment agreement is questionable.
If the builder attached rent receipts in your grandfather’s name (not your uncle’s), that strengthens your case that tenancy was never transferred exclusively to your uncle.
If your uncle was not the sole lawful tenant, he could not will away the entire tenancy/redevelopment flat.
Under Hindu Succession Act + Maharashtra Rent Control Act, your mother being a Class I heir of your grandfather has a claim in the tenancy rights.
Since tenancy was not formally transferred solely to your uncle, your mother can challenge the redevelopment agreement.
She can demand her share in the redeveloped flat or compensation.
File a suit in the Small Causes Court (Rent Act jurisdiction in Mumbai) or City Civil Court, seeking:
Declaration that your mother is a legal heir of the original tenant.
Injunction restraining builder/uncle’s family from excluding her.
Partition of tenancy rights in redeveloped flat or equivalent compensation.