Board Thread:Questions and Answers/@comment-30300307-20170426071235/@comment-679780-20170428200842

DerpyShadowFan1234 wrote: My theory is that the Chaos Emeralds become Super Emeralds only in times of extreme peril and dire need. In S3&K, I think Eggman was experimenting with the Master Emerald to create... something. Something so powerful, it threatened all life on the planet. I think he almost finished, but Sonic used tthe Super Emeralds to stop him.

I think he was creating Solaris. I believe the first time the Chaos Emeralds became the Super Emeralds, they took on two transformations:
 * They grew in size, becoming almost as big as the Master Emerald.
 * They changed in shape, becoming diamond cut.

After the events of S3&K, the Super Emeralds became the Chaos Emeralds again (return to normal size) but still retain a portion of the power they once had (retained their modern Diamond Cut shape) and this is because why since then Super Sonic has become almost as powerful as Hyper Sonic.

I'm honestly alright with Hyper Sonic being removed from canon given on modern games he would be ridiculously OP in comparison to modern Super Sonic, but I disagree that he is indeed removed, just perhaps unlikely for the Chaos Emeralds to become Super Emeralds in the future.