When Ken was taken over by the powers of darkness and became the Digimon Emperor, the evil that turned him bad also hid the Crest of Kindness. Even though it was hidden, the crest was still powerful, and Ken still was drawn to it. He didn't know why, but it was able to power his base.
The ones who want to restore harmony to the Digital World (Mentioned in "The Ultimate Clash" and "Kyoto dragon") found that the only way to release the Crest of Kindness was to rebuild it as the Digiegg of Miracles. Ken couldn't recieve it as the Digimon Emperor, so it's had to be used against him to return him to his true self.
Like the other Digidestined, the crest will glow in a moment when the Digidestined is showing the quality their crest represents. There was a doubt that Ken's crest actually belonged to him, until his true kind self came out (in that sweet Primary Villiage scene) and it glowed!! ^__^ The Digimon Emperor was gone for good and Ken's true kind personality shined!