no no, you've got it wrong. when they travelled to the future they had already changed it by saving claire, thus her being alive instead of dead as future hiro thought. so Peter had saved claire in this timeline. the reason sylar wasn't dead in this future was because they had travelled forward before hiro got the chance to stab him yet in the 'standard' timeline, so of course, he will still be about in the future. basically, time travel is insane and makes no sense. but, it's fun. this is why The Doctor never _really_ messes with time and why the writers have this 'we are part of the timeline and cannot change events' clause - because otherwise the entire logic of the show would break down.