In the Season 5 and series finale:
Walter takes Micheal (the child observer) into the future so that the scientist realizes that superior intelligence and emotions can coexist, and the observers are never created.
Earlier on in the series we learn that:
Walter loses his Peter in the primary timeline, and then watches as September distracts Walternate and unintentionally prevents him from curing Peter. Due to this, Walter crosses over and brings Peter to the primary timeline. However, they fall into the lake and are rescued by September.
So wouldn't all this not happen when the Observers no longer exist?
Wouldn't Walternate discover the cure, and hence cure Peter in the alternate timeline, making sure that Walter never crosses over, and Peter never comes to our timeline?
This would mean that Olivia and Peter never meet, and Etta is never born. So how is it possible for the time reset version of our Universe to still show them as a family?