DC Comics' the New 52 may have reinvented some characters well, but the ratio between pros and cons heavily favored more the cons. Amongst the heaviest hit were those of the original Young Justice. All the members had their origins radicalized to edgier tones and barely resembled the character they once were over in Teen Titans. None so much then Superboy Conner Kent.
To even explain the character's New 52 origins is a convoluted and complicated mess. If I even mentioned a piece of it you or probably I would resort to drinking to repress the horrific writing. To say the least putting the character along with the other members of that team on the back burner during Rebirth had to happen given how badly DC screwed it up with all of them during the New 52.
Currently, over in Detective Comics, Tim Drake is getting his origin patched up and the New 52 deadweight being tossed out. At NYCC at the Batman panel at NYCC today, the writer for the comic James Tynion IV said that "we'll find out in upcoming issues." (i.e. it has since been narrowed down to Detective Comics #966) And has been asked this question repeatedly by fans. DC then backed up that with their tweet:
More than likely this is due to in the first Detective Comic arc by Tynion, Tim was placed in a cell adjacent to two other cells. Much debate was placed on the character's cellmates being his former comrades of Young Justice/Teen Titans.
That fire continued to burn over in Action Comics during the Mr. Mxyzptlk arc where the continuities of Superman (old and New 52) are merged save one exception. A lingering doubt from Superman that something still was missing. That one thing missing? Conner Kent, as "Reign of the Supermen" was restored.
Now it looks like we'll be getting an answer. Of course, this begs the question: if both characters are getting their origins retooled back to their old ones does this mean we'll be getting Young Justice Rebirth? Since we kind of have two teams of Titans running around.
I guess we'll just have to stay tuned...