There are two answers to this particular question, and they’re both rather interesting. The simpler answer is that we’ll probably see them in Sonic The Hedgehog 2, as that film will probably want to go off world to explore more of those safe zones Sonic had earmarked for potential escapes. Since Robotnik is in one such world, he might already be discovering them as we speak. However, if the concept art that was leaked from the film has anything to say, the Chaos Emeralds might have existed in a previous draft, only to be written out of the film in later revisions.