For the last 300 years of the “Pharaohs” NONE of them were Egyptian. They were all Greek. The Ptolemaic Dynasty ruled Egypt from 323 B.C. to 30 B.C.. The first “Greek” Pharaoh was Ptolemy I, a commander serving under Alexander the Great. After Alexander’s death in 323 B.C., Ptolemy became the Pharaoh of Egypt. For the next 300 years in Egypt, every ruling male was named Ptolemy and every ruling female was named Cleopatra. To distinguish them from one another, each was given a number after their name. Virtually all of the Ptolemaic Pharaohs were produced by inbreeding. This was the way power was kept consolidated in the family.
With Julius Caesar dead, his nephew Octavian and friends Mark Anthony and Lepidus jointly ruled the empire. Cleopatra and Mark Anthony met, fell in love and married (Anthony was already married). They had three children together. Twins were born in 40 B.C., a boy, Alexander Helios and a girl, Cleopatra Selene II. Four years later, they had another son, Ptolemy Philadelphus.
All three children of the couple were spared their lives. The twins were 10 years old, little Ptolemy Philadelphus was six. They were taken to Rome to live under the care of Mark Anthony’s Roman wife, Octavia Minor, who was now also a widow.
So now we have some closure to the question of what happened to Cleopatra’s children.