Well, they saw him now though and this was before his father was sent back.
Sharidan is talking about John being dead in the episode about the submarine. Cameron was very adamant about passing all info to John, and Jessie said no one had seen John for a long time.
John came to the future at a point long before the submarine episode.
I think Cameron might have killed him, and perhaps she is an impostor, and she wanted the metal bot to join her "revolution"?
Remember, Cameron was a human, she was killed by the robot Cameron, and replaced.
It was hinted that Cameron could have been Johns woman. Maybe the she-bot Cameron killed John and took over the human resistance in his place?
You know, if machines really did become self-aware, they would probably split into different groups, and most likely even war with each other, just like humans have.
The big difference is that what takes man several thousands of years to get to a warring point, it would take a super computer only a few milliseconds.
Mankind at this point is just a nuisance to the machines.
(Anybody ever read "Of men and monsters"?)