Its possible, but I never really felt it was that thoroughly foreshadowed personally. Isn't that often argued because of the early Reborn suggestion that there were still problems with the timeline? but if it was supposed to be a thing directly concerning Conner, it was really last minute because references to Reign in those crash course history lesson issues in which the vague discrepancies were teased, the artist actually drew Kon in originally but had to go back and remove him. So maybe they said, "wait, lets say there's still issues with the timeline and get rid of Conner for a while to accentuate that". But it would be weird if they decided that, lay the foundation in Superman, and then end up it being more of a Tim Drake journey. But then again they do stuff a lot that doesn't make sense. Either all this or they just got rid of him to promote Jon. I think either or is equally possible. That said, even if its the latter, the question still remains was Bendis the one who eventually backed his return? Those things don't necessarily have to go together either.
TL;DR I really don't know either.