Whether the JDA was a registered document, before the jurisdictional sub-registrar, if so, take a copy of the same to an advocate nearby get the agreement read over properly for seeking a legal remedy against the builder. The terms and conditions of the JDA form the basis in determining the extent of damages or compensation you can claim from the developer.
Whether the JDA was favouring your mother or not cannot be questioned by you now, but whether the terms and conditions are fulfilled by the developer can definitely be questioned by you before the jurisdictional court (if arbitration clause is not provided in the JDA).