I like the theory of there being two sets of Chaos Emeralds, at least to a certain point. I see it as this: Dr. Robotnik steals Knuckles' set, convinces him to think Sonic stole them, causing Knuckles to steal Sonic's set. Robotnik hides all of Knuckles' Emeralds in the Special Stages, which is what Sonic collects. Knuckles' Emeralds are then powered up by the Master Emerald into the Super Emeralds. Permanently. Sonic's Emeralds continue to be Chaos Emeralds, and the same ones used throughout the rest of the series.