Property Registration Dispute

My father's brother has a 3-floor property in his name. In that, the 2nd floor was built by the contractor using his expenses. My father later paid the entire amount to the contractor and started living on the second floor. Since the property has a housing loan second floor could not be registered in my father's name. But, the contractor has made an agreement stating the same. My father's brother (building owner) has also signed the agreement as a witness. Now my father wants the second floor to be registered in his name, but my uncle is not willing to register it. What can be done.