If the royal guards in the prelude had taken anything and everything not native to the Everfree Forest from the clearing where the cult worked its spell, how were Twilight Sparkle's saddlebags still there for her to find in the next chapter?
In preparation for the final three chapters, the authors did a second, less-severe revision. This time, the guards were more concerned about the clearing itself and the cult had previously tossed the bag futher in the bushes, where they were overlooked.
Twilight Sparkle had been ponynapped by a cult, and was told in no uncertain terms that their intent was to bring back Nightmare Moon. She never forgets this fact. Why then, before she even finds Nyx, does she not tell Princess Celestia what the cult's plan was?
In preparation for the final three chapters, the authors did a second, less-severe revision. This time, Twilight never got to hear what the plan was, so Celestia and those she put in charge of the investigation found out before Twilight did. Twilight forms her own opinions based on the power she felt when the spell was cast and what Nyx looks like but it's only when Celestia comes to take her away that she learns the full truth for herself.
If Twilight Sparkle suspected Nyx was Nightmare Moon, but didn't want harm to come to her, why didn't she use the elements of harmony? If it was NMM pretending to be good, she'd have saved Equestria a lot of trouble, and if there was a genuine bit of good in Nyx, the rainbow of light would have let it stay. And don't say Nyx is made of dark magic, knowing Twilight and her mastery of magic, she would find a way to make the rainbow of light let Nyx's good side live.
One could argue that Twilight did not want, choose, or think to use the Elements of Harmony because they are very ancient power that only Celestia and Luna could properly understand. After all, Twilight only just figured out the sixth Element of Harmony in the last few minutes of the two-part pilot, so she probably doesn't know nearly as much as you might think she does.
"Knowing Twilight and her mastery of magic, she would find a way to make the rainbow of light let Nyx's good side live": Twilight is a talented spellcaster, but she doesn't have total control over every aspect of magic. The only thing she knows how to do with the Elements is to use them as a shotgun with "Point This End At Evil" written on it. If Twilight gathers up her friends, points the Elements at Nyx, fires and messes up even a little, Nyx dies. Not a particularly heroic action, really.
Twilight tells Nyx to think of her as a mother, and goes for the whole adoption route. Did Twilight forget the part of the cultists' spell where they use her blood? If we follow how Nyx was created from her blood, then Twilight actually is Nyx's mother genetically.
Two things: one, Twilight had a bag over her head, so she probably doesn't know what her blood was used for. Two, one might argue that the drop of blood was merely a catalyst for the spell. Some might even argue that the drop of blood is more in tune to a blood transfusion. I'm pretty sure that donating blood to another person doesn't make the two related.
The blood transfusion bit doesn't really apply here. There's a difference between a small amount of blood being given to a person and a person being born/created/whatever with the blood as a base. Also, from the sounds of things it wasn't a catalyst, just Nexus trying to find a way to prevent the Elements of Harmony from working. Beyond that, it's open to interpretation. Anyone know if there's been Word of God on this issue?
The authors (or at least one of them) has claimed that that Nyx isn't genetically related to Twilight. Considering they're really pushing for a "Nyx is Nightmare Moon reborn" story with their last edits, this might be another item that get's revised.
Spell Nexus stated that he himself received "the blessing" from the remains of the originial Nightmare Moon, suggesting that "the blessing" is responsible for Luna's transformation into the original Nightmare Moon... and now it's spreading.
In the original edit of the story, Celestia took Nyx away from Twilight with the intent of testing to see if she was really Nightmare Moon—- and if she was, using magic to dispel her into oblivion. That's right; Princess Celestia was going to disintegrate a little filly into nothingness. This was so fridge-horrific, not to mention out of character, that the authors subsequently retconned it.