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It’s interesting that you see absolutely nothing of Chrysalis before or after this part in the Manga.

In fact, while you initially see changelings after the main timeline was altered from the Elements of Harmony being stolen by Discord in the past for the scavenger hunt, they conveniently don’t exist, to the point it feels like they’re (along with Chrysalis) entirely forgotten about for either the action scenes taking place when this timeline is returned to (Nightmare Moon brings out a “bugbear detachment” instead of any changelings, after the individual alternate timeline quests, or the resolution where Celestia gets freed (with Luna of course noticing her tan) and they reconcile.

It’s frankly jarring how meaningless this setting detail is as exposition, because not only does it never factor into the plot (Nightmare Moon could’ve taken over anyway as presented by canon, as far as the show went), but it seems rather OOC for both parties involved to be willingly working with a similarly power-hungry villain without some pressuring involved, or backstabbing (or the lack thereof) mentioned. You could take it, and the random changelings out, and there would be less questions raised.