The sale agreement is also done by an unregistered document, hence any manipulation can be done by you father in connivance with the builder.
Therefore you may issue a letter to the builder to not to entertain any such claim from your father in future in this regard failing which can hold him responsible for legal consequences for breach of contract, breach of trust, cheating and other related criminal offences.
You can get the letter drafted through an advocate to make it more effective and strong so that the builder will not dare to be in hand in gloves with your father in this deceitful act against you.
You are right that the agreement for sale is valid and effective only for three years, hence you can get the agreement renewed at the end of the third year which will have fresh lease of another three years from the date of renewal.
For the purpose of having a sale deed on your name, you can get a unregistered sale agreement duly notarised along with the possession of the property and make sure that there is a recital mentioning that the builder shall execute the registered sale deed in your favor when the GHMC is regularizing the construction of this unauthorised house/flat constructed on the fourth floor.
This deed and the possession of property may come to your rescue at the time actual registration if the builder is refusing to do it at that time.