The Chaos Emeralds' early history was most likely largely the same as their Mobius Prime counterparts'. The point of divergence was when Knuckles became corrupted by his chaos powers and decided to conquer Mobius.
In order to combat the growing threat of Knuckles, now having assumed the mantle of Dark Enerjak, Sonic the Hedgehog gathered the Chaos Emeralds and used their power to transform into Super Sonic. Unfortunately, he was defeated by Knuckles, who took him prisoner and claimed the Emeralds for himself, ensuring that no one would ever be able to use their power against him again.
It is indirectly stated by Sonic on his draft on the Archie Comics blog that the Chaos Emeralds appear to have been reduced in number to seven, like on Mobius Prime. As such, some version of the Great Harmony appears to have taken place following the beginning of Knuckles' descent into madness.