The part about the human dna in Conner being altered was likely a way of Geoff Johns to connect his new origin (clone of Superman and Lex) with his first origin (a human clone altered).
However, his human dna being altered in Conner's new origin wasn't really important and was mentioned only once. It was totally ignored and forgotten after that.
Now, it is pretty likely that DC (and writers) has completely forgotten (and retconned too) that aspect. DC likely consider Conner a human-kryptonian hybrid like Jon.
That's why they threat Conner as baby of Lex and Clark.
PS: Even if Conner recovers all his story (which seems unlikely), the part of "human dna altered" won't likely return.