How come when all the robians but Sonics dad was deroboticized, bunnie still remained half-robian like always?
Simple answer is that the Bem never took Bunnie. The answer that you are probably looking for is that it is assumed that the Bem’s machine does not work on anyone that is part-metal, part-flesh. It has only turned fully-flesh beings into fully-metal or fully-metal beings into fully-flesh. Anyone that is part-flesh and part-metal probably could not use the machine.