Sci-Fi magazine SFX has an exclusive interview with Fringe executive producer David Fury, in which he tries to explain what happened to all the timelines in the Fringe series finale "An Enemy Of Fate":

“Here is my take on it: we are still in the revised timeline where Peter died as a child. The dystopian future was the future of the timeline of season four, therefore Peter did die as a child in this timeline. However, we know he reappeared in this timeline in season four and became part of this family. Then Olivia regained the memory of the erased timeline, so she remembers seasons one through three even though she didn't really experience it in the timeline. The same with Walter after Michael touches him in season five, so now Walter remembers it. So they have a shared memory of seasons one through three but the life they are continuing is the life presented in season four. As far as what happens when Walter and Michael step into the corridor to the future, our premise is that the change happens – and it’s the part that is inexplicable but go with it – once they step through Walter and September stop existing in the timeline. It’s not that they never existed. They still experience the events of season four and still have all the memories of the earlier seasons when the timeline hadn't been erased, however they stop existing at the moment of the Invasion. It’s not like Walter died. Peter is just going to find Walter missing. He’s not going to be looking for September because he didn't continue their relationship, just Walter did. When he looks for Walter, he just won’t be there because this corrects the paradox. It’s somewhat nebulous but that is the premise of what we did.”

How does that explanation match up with your understanding of what happened?

For the rest of the interview, check out Fringe: The Unanswered Questions Answered, in SFX: Issue 234 on sale now.