Actually, according to Terminator Director Joseph "McG" Nichol, Skynet is fully aware of the fact that Kyle Reese is John Connor's father by the events of the fourth Terminator film.
This is strongly evidenced by the fact that Kyle is at the top of its kill-list and by the fact that its infiltration agent (Marcus) seemingly knows that Kyle Reese is John's father.
McG doesn't go into great detail other than to describe it as part of their "recon".
Q: In the earlier movies, Skynet is not aware of Kyle Reese. So, why
are they aware of him now?
McG: It’s a function of their recon during the dark period, and a
function of their awareness of the events that had happened since Kyle
Reese traveled back. By virtue of John Connor being alive, that means
Kyle Reese did meet Sarah Connor and impregnate her. That data exists,
and was brought into the fold at Skynet.
My personal theory is that since the Terminators are able to communicate with (future) Skynet by leaving time capsules, there's every chance that they've submitted mission reports, images, DNA samples, etc that Skynet could analyse at its leisure.