Actually, the main issue here is that the two worlds somehow merge and are thrown together. I'm going to assume that they're suddenly thrown onto some alternate earth/designed planet. Their pasts could not co-exist, and therefore, the time travel bit is out AFAIC. They were created under very different circumstances, so I'm not sure how we're going to assume that only the Matrix past timeline exists.
Secondly, Skynet couldn't even kill ONE human or her son in the past. Clearly there ability to time travel isn't unlimited, and if they can't manage that, I doubt they could pull off the entire series of events necessary to stop the Matrix machines from coming into existence. I do not believe that the machines could manage to simply wipeout Skynet either given that for both timelines what has happened in the past is murky.
The humans in the Matrix and the Terminator series, as well as Skynet itself were unable to determine the sum total of events that led to their "current" existence. The time travel victory premise is entirely out of sorts in every way for this scenario. Just leave it alone.
Sticking with valid points that have already been discussed at length in the original thread, the machines wholly destroy skynet.