@Scrounge  
Celestia is a pretty big deal to her and Twilight. You don’t just forget people like that. If she considered her important enough to banish to the moon along with her sister, I’m pretty sure she’d remember her.

@PumpJack  
Even if she just picked the wrong time and place to not sell out, rather than actually being important?

@Scrounge  
Nightmare Moon would have recognised Twilight were that the case.

@PumpJack  
Either that, or Twilight was so unshakably faithful to Celestia that she received the honor of being imprisoned with her.

@Baskerville3  
Zecora said it in the episode.
 
“The smallest changes could lead to a cascade of effects downstream”. i.e. Butterfly Effect and multiverse theory.
 
All timelines result in Twilght and her friends never coming together, but that doesn’t necessarily mean that they’re the only ones who are able to wield the Elements and stop the villains. Celestia defeated her sister and banished to the moon, what’s to say that she wouldn’t be able to do so again? What if in the third timeline, Nightmare Moon successfully returned, and made a truce with King Sombra to keep Chrysalis and the Changelings out? Or what if there were other ponies who were worthy of the Elements of Harmony to take their place?
 
There are infinite possibilities with infinite answers to infinite problems in infinite scenarios- so while the event to kick them all off is the same, the outcomes could be vastly different.

i still ask how does the timeline shifting and what villain taking over, makes sense!

@Shritistrang  
Twilight becoming Nightmare Moon’s protege instead of Celestia’s?
 
Now that’s something I would like to see.

Now I wish to see what would have happened to Twilight in the Nightmare Moon AU.

Well done!