Thread:SonictheHedgehog1245/@comment-26897822-20170123204417/@comment-24908786-20170127030659

My guess is that Star Swirl's spell protected them from the changes to Equestria's space-time continuum with each time Starlight altered the past.

Either that, or the Tree of Harmony because of the map. It existed in all the altered timelines, so the Tree of Harmony knew something was wrong.