I'm wondering if it might be a good idea to actually put some kind of zebra cataclysm into Nightmare Moon's backstory.
Something which might justify the legend and extreme superstition that they hold against her.

5956177 , I don't know. That might just make things more complicated. I mean, then you'd have to fill in something else to re-justify Nyx's standpoint which would require another backstory point to justify the zebras' standpoint, etc. Before you know it, you're not even writing a story anymore. You're just filling in concepts and ideas in a giant "he-started-she-started-it" conflict to the point that anyone reading it all gets lost... and no wall of text is going to reel back in a confused/disinterested person.

5956177
You could certainly elaborate on it when Flitter goes to rescue Zecoras sister. You could even tie it into the ancient cataclysm that heralded Hyperions war against ponykind. Old stories and such depicted in Zebra art and tradition.