I've made no secret of the fact that I found the entire invasion plot in season 5 rather lacking and not very well thought out. No explaining the reason behing the invasion is a serious problem for me. For me, one of the big consequences of not anserwing that question is that it makes me wonder....why didn't the Observers invade the first time? In the "Day We Died" we visit a dark alternate 2021 of the blue universe. Yet in that 2021, the Observers never invaded. The original 12 are still wandering around so their timeline is in tact, but they never invade. One wonders why?
The only thing I can think of is the existence of Henry. September explained that Peter having a child with the wrong Olivia creates a son instead of a daughter and prevents the future he came from (which is why the Observers wanted Peter to wink out of existence). They never actually explain what it is about Henry that prevents the existence of the Observers, and I imagine he was killed along with the rest of his reality in that alternate future.