In act four, after John makes pardox clones, Karkat has a pesterlog with him. In it, he states that unless they had achieved this part in time, they wouldnt had existed. If so then how did the rose and dave doomed timeline occur? Wouldnt they become non existent the moment that John was killed? Or are there shenanigans at play?

That would have been one of the reasons it was a doomed timeline.