Wolfenstein - The first 2 games carried franchise name Castle Wolfenstein, with Wolfenstein 3D dropping the “Castle”. Later sequel, Spear of Destiny, missed the Wolfenstein name entirely, only for it to be picked up again with Return to Castle Wolfenstein.

Alien/Predator - Starting off as two separate franchises - Alien and Predator - these later merged with Alien VS. Predator, but the later prequel, Prometheus, had neither of the both original franchise names.

Heretic/HeXen - Originally called Heretic, with the sequel changing name to HeXen: Beyond Heretic, with HeXen II continuing with that franchise name, only for it to be reverted back with Heretic II.