In the fringe season 4 finale, Jessica Holt used some sort of technology to block September such that he was unable to shift, or even move. Why was this technology not used in the war against the observers? This would have won them the war. Yet the technology is never even mentioned again.
September says in that episode
I am surprised they knew of this methodology. It is... beyond them.
So maybe the "stasis rune" (that's the term used for it) is actually a piece of Observer technology that William Bell obtained somehow. In that case it would be unlikely that when the Observers took over the world, they would bring more stasis runes from the future, since they're strong enough to incapacitate them.
It's probably mainly down to Fringe originally being intended for 7 seasons, then getting cut to 5. A lot of questions may have had answers that were cut to fit to the shorter season count.
In-universe, I think we can kinda agree that Bell only used the stasis runes to get to Olivia, not the Observers themselves. And thus, when the invasion came, he may still have been the only person with knowledge of the technique, and what with Walter's ideas of Bell selling them out to the Observers, it's possible the resistance never heard about the runes.