We now have all of the events between the 1984 arrival of the T‑800 up to the point where Kate sends a reprogrammed T‑800 back to 2004 in one continuous timeline. As we have avoided all paradoxes and resolved all potential conflicts, we believe we have succeeded in what we set out to do.
All of these events can happen with no other changes to the past to be accounted for and we can move on into the future. What that future holds, we do not know. Perhaps Kate will attempt to find a way to prevent John's murder.
The next thing I'd like to talk about is the irony of the effects of Skynet and John messing around with the past. Skynet's goal is to change the past and John's goal is to preserve the past, however, the effects of their behavior end up being exactly the opposite.
When Skynet sends Terminator's into the past to prevent John's birth and end the resistance, it has very little effect on events. In Chronology 2 the arrival of the T‑800 does not effect future events at all. Sarah is even unaware that a Terminator has arrived to kill her. Skynet, Judgment Day and Sarah's rise to leadership all occur in the same sequence and at the same time as in Chronology 1.
In Chronology 4, where we view the changes by the arrival of the T‑1000 in 1994, we also see that his has no effect on events. Skynet wants to kill John and end the resistance, but John never actually encounters the T‑1000 and may be completely unaware of its presence. Cyberdyne, Skynet, Judgment Day and John's rise to leadership are unaffected.
However, the effects by Sarah, John and Kate sending people into the past causes major disruptions in the sequence of events. When Kyle arrives, he not only becomes John's father, he gives Sarah detailed knowledge of the future which radically alters her behavior, completely changing her life, and Cyberdyne ends up obtaining the parts from the T‑800 which leads to Judgment Day occurring at least 7 years earlier. Also, it is through his intervention that Sarah ends up crushing the T‑800 and getting exposed to radiation which leads to her death.
When the reprogrammed T‑800 arrives in 1994 it leads to the death of Myles Dyson and the destruction of Cyberdyne and completely changes when Judgment Day occurs. Admittedly, John's first decision to send this T‑800 back was indeed intended to radically change events rather than to preserve them, but is was these changes which eventually lead John to modify his behavior and begin to rationally deal with the effects on the past.
Ironic as this all is, there is a more important point. The reason that Skynet's effects were so much less than John's is that Skynet missed entirely what John realized quite quickly. It is not the visitors from the future which have an effect, it is information from the future. To Skynet, killing Sarah will achieve its goal. To John, telling Sarah things will have a much more profound influence.
The passing of information from the future to the past is what really changes things and why, when John finally realizes that his actions are radically changing the past, he begins controlling the information he is sending back, modifying it so as to not have an effect, otherwise a never-ending series of changes could occur, each one potentially worse than the last.
Skynet never understands this, it is too mechanical in its approach to the world, which, in part, is why it will always fail when it battles humans and is the hopeful message these stories pass on.