Okay, I'm trying to work out what could have happened in the original timeline up to "Five Years Gone" here.
Sylar gets to Claire at Homecoming and kills her, gaining her regen powers.
Claire comes back from the dead after this and Bennett hides her away.
Peter never meets her, never gains the regen powers, thus allowing him to get that massive scar across his face.
Hiro meets Sylar in New York, and after Ando is killed, stabs Sylar with the sword.
Sylar regens and runs.
Peter explodes killing most of New York.
Nathan blames it all on Sylar and rides this into power.
Specials get outed, and hunted throughout the world.
Bennett sets up an underground railroad, and Hiro funnels Candace and DL through that.
Sylar gets to DL and Candace, kills both and takes their powers.
Using Candace's powers, Sylar kills Nathan and takes over his role.
Hiro has managed to change the past then. By getting Peter to Homecoming, he stopped Sylar getting Claire's regen factor. Just as when he went back to Charlie, he's managed to make a small change in time, but the general flow of time keeps going.
Though the fact that Peter has a scar, and yet Sylar still seeks Claire's regen powers seem to contradict each other.
My head hurts.
Heroes sidenote. Calling these two wacked out theories now :-
1) Ma Petrelli has a power of prophetic dreams. Peter's been demonstrating these powers over the season, so he had to pick them up from somewhere.
2) Charlie was going to die from a brain