I'm betting on the fact that since the Observers are basically one HUGE paradox, Walters plan will get rid of the paradox and rewrite time to the point when the invasion started. Or, you know, The Doctor will fix it.
In my head cannon, Journeys End never happened, Donna is still traveling with the Doctor, and Rose teamed up with Olivia to escape the alternate universe (The filled with zeppelins universe)preventing Altlivia from sleeping with Peter.