Well, they do in canon...

Clark and Lois go back in time in TF and baby CK is there - Clark even holds him at one point and takes him back to the spacecraft.

Maybe it's different because it's back in time instead of forward...?

However, if the little CK doesn't get back to his own time, before long our CK will start to disappear a la Marty in Back to the Future or even Clark in TF because the past has been changed too much. How long that window is... well, that's up to our author I suppose smile .
Carol