How is the legal inheritance of real estate divided among the heirs, and are the two apartments built by the eldest brother from his own money deducted from it?

Merely granting permission to build does not establish a gift (hibah). If your father did not explicitly gift the air rights to your brother, then what he built is considered a loan (ʻariyah) which terminates upon the father's death. What he built should then be appraised, whether it is dismantled or standing, and the heirs pay him its value and take ownership of it.