It appears your mother's brother has attempted to make capital out of her age and lack of knowledge regarding the legal process of obtaining a partition deed executed and registered. Section 17 of the Registration Act, states that any partition deed related to immovable property requires registration for it to be considered valid. Notarization does not cover legal enforceability in matters related to property. This is most especially true when co-owners' rights are involved.
In your case it appears that a deficiently stamped document, following the payment by your mother's brother of shortfall stamp duty levied with section 40, Indian Stamp Act, caused the document to become registrable. Stamping requirement does not become the consideration of validity by the parties making the transaction though consent for executing was fraudulently obtained.
If she signed the partition deed under coercion or misrepresentation or without understanding what the contents mean, there is a legal basis for challenging its registration. The Supreme Court, in Krishna Mohan Kul v. Pratima Maity, noted that documents executed under fraud or undue influence are void and can be set aside by the court. Further, Section 31 of the Specific Relief Act, provides a remedy for cancellation of such instruments when they adversely affect legal rights of a person.
Given the facts of the case, a civil action for cancellation of the partition deed seems to be the proper remedy. The court will examine whether your mother was given her free consent and whether the deed was executed in good faith. Evidence of her advanced age, lack of legal advice, and other facts indicating manipulation or coercion must be presented to the court.