I was thinking about Jack saving Charlie's life and realized that very early on in the show Charlie actually saved Jack's life. Remember Moth? Jack gets trapped in the caves and Charlie goes in to rescue him. Now we see Jack saving Charlie's life. I think some things in this new timeline will reflect things that happened in the first timeline. Some may happen the same way and some may happen differently. For instance, I think Kate is still going to have to deliver Claire's baby in the new timeline for some reason.
Hold on, just had a new thought. Jack also saved Charlie's life when he was hung by Ethan. Resuscitated him even after Kate was begging him to stop. So it could be reflecting that event too. I think a lot of events in the new timeline are going to reflect events from season 1 is my main point I guess.