I'm going to use the Doctor Who explanation for inconsistencies, and say that in a series that allows for time travel and paradoxes, things can change. There's 8 Chaos Emeralds? Someone obviously changed something with those Time Stones. And so on.
Nevertheless, I have worked out my own ridiculously complicated 'canon' - although I hate that word - which is a mixture of Fleetway, game, and my own thoughts. The Drakon came into this dimension in an attempt to contain Chaos, using the Echidna's emerald deposits. However, on the way back to their own dimension with the new emeralds, they were attacked by a bunch of vicious, Monty-Python-rabbit-like Chao. A few generations later, the Echidnas attempted to take the emeralds back, but Chaos attacked, and most of them were wiped out, leaving only a few. These emeralds were stolen for a time a while back by GUN, during which time all the Shadow stuff was done, and so forth, leading to additional paranoia about thefts from the Echidnas (or Echidna, by the time of the games). Then there's another, manmade set of emeralds created by Eggman with the ROCC, based on Gerald's notes and so forth, eventually combined with the 'real' ones.
All of the above is, of course, nonsense. But entertaining nonsense, I like to think.