It can't work period. Just like initiating a global invasion 150 years before the initial experiment that created your "race" wouldn't work. This episode was really bad, but the timeline stuff is horrible. Anyways, if/when it does work, Peter will never leave universeB, Fringe Division will never exist, and Walter (if he still gets committed) will never leave the mental institution. Peter and Olivia should have figured this out immediately, and realized that they won't get their daughter back. Wouldn't be so bad, if say, the initial experiment had occurred before the invasion and if September hadn't distracted Walternate that day. Also didn't like the retcon of "The boy is important, he must live." Ugh.
Was hoping "the plan" was to build some sort of device that would send out a pulse that would fry Observer implants.