Nothing except the Greek name and they both get a mention in the Iliad. In Egyptian Thebes is called Waset meaning the city of the sceptre. The greek name comes from the temple complex at Karnak across the Nile which in demotic Egyptian is ta-pe which eventually came into Greek as Θῆβαι. The Greeks distinguished between the two cities by called Egyptian Thebes "Θῆβαι ἑκατόμπυλοι" 100 gated Thebes from the Iliad. Greek Thebes is called "Θῆβαι ἑπτάπυλοι" seven gated Thebes, also from the Iliad. Incidentally there is also another city in the Iliad called Cilician Thebes under mount Plakos. Andromache the wife of Hector was born there and her father Eetion and her brothers were killed there by Achilles.