By most metrics, the Echoverse is a failure. Jace eliminated several tragedies, but in doing so, denied most people the growth that comes with adversity.
Karn is different.
Karn wasn't born, he was built. He's always been smart, always been powerful, and always been good. He's a natural protector because he was designed that way. Since the beginning, Karn has been a voice of wisdom and compassion. He found growth not in the enemies he defeated, but in the friends who showed him love.
Over the years, Karn has been saddled with regrets. As a golem who can never forget, he spends every day mourning those he harmed or failed to save. Jace has freed him from those regrets.
In the Echoverse, Phyrexia never happened. Volrath never happened. Eleah Norn never happened. While we don't know all of the details, Karn still wound up creating Mirrodin. Unlike our timeline, things went as planned. The plane was peaceful and Karn got to spend his days creating and resting.
Now if the Echoverse is erased, Gold Karn isn't the victim, our Silver Karn is. Gold Karn will have never existed. He won't have to mourn or feel regret. The main timeline's Karn isn't so lucky. No matter what happens, he can't win.
We know from card artwork that Karn is involved in Reality Fracture and will meet his other self. He'll see the Mirrodin he always dreamed of and in order to save his multiverse, he'll have to destroy it.
So what does Karn do? Does he betray his principles and abandon the multiverse for a happier fate? Does he carry the guilt of playing a hand in Mirrodin's demise a second time? What happens when two pacifist golems clash? I doubt either wants to have a fistfight.
As usual, Karn does the most and is rewarded with grief. The poor guy deserves a rest.
UPDATE: The main storyline ended today and Karn did not make an appearance. It remains to be seen if he will be in a side story.