All perfect praise be to Allah, The Lord of The Worlds, and may His peace and blessings be upon our Prophet Mohammad and upon all his family and companions.
If a father agrees to allow one of his sons to build over his property, then this is permissible, and both parties should honor that agreement. Moreover, the father may allow his son to do so under the condition that the built flat becomes the son`s own, except the roof. In this case, it is the right of the son to lease that flat which he has originally paid for after having obtained his father`s permission. This opinion is based on the Fatwa of Abdullah Ibn Mas`oud as reported by Al-Baihaki, and it reads as follows: "If a person builds upon a land after having obtained the permission of its owner, then the value of that building belongs to him."
However, after the father`s passing away, all his possessions become an inheritance of his heirs. Therefore, the son can keep his flat under the condition that the value of the roof, on which that flat was built, is deducted from his share in the inheritance, or he may take the value of that flat, except the roof, in case the whole building was sold, then take his share from the rest of the property`s price. And Allah knows best.