A while back, we reported via a third party interview with BigRedButton head Bob Rafei that Chaos Emeralds would not be a part of the side universe established by Sonic Boom.
Late Tuesday on the Sega forums, Sonic Boom producer Stephen Frost clarified remarks made in that interview:
I just wanted to clear something up about the Chaos Emeralds as I think there was some initial confusion based upon an answer that Bob gave during an earlier interview. I believe he just misunderstood the question. When he said that there were no Chaos Emeralds, he simply meant that they do not appear in the upcoming Sonic Boom games. And there are specific reasons for this. However, that is not to say that they couldn’t exist within the overall Sonic Boom universe. I can’t promise that they will be talked about or brought up anytime soon (or at all) in any aspect of Sonic Boom, but there is nothing that prevents their possible existence. Just wanted to clear that up for you all.
The bottom line: For the moment, just because they won’t appear in the Sonic Boom game does not mean the emeralds do not have a role in the overall universe mythology. But whether Sega personnel will, through speech or otherwise, confirm that role, is anyone’s guess.
http://www.tssznews.com/2014/04/23/sonic-boom-producer-clarifies-chaos-emeralds-role/