I believe I remember that, in Season 4, we saw several times that once somepony was released from an evil enchantment, this energy would go away.
I was expecting the season 4 Finale to be about some monster or entity that was collecting this energies, but it wasn't.
I was then expecting the season 5 Pilot to be about this same entity, but it wasn't. And with the villain getting away, we can easily suspect the next season Finale to be about this same villain being finally captured.

So, anybody else been bothered by these energies?

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Well, not really. If there was some kind of will behind all this dark magic, like the Nightmare Forces in the comics, then we'd have a problem, but dark magic by itself just stuff. Energy disperses and is converted into other forms. There's no reason to think that all the dark magic ever seen is still hanging around and waiting to do something nefarious. In the case of intact artefacts like the Alicorn Amulet and Sombra's horn, yeah, those could still be trouble, but only if they got into the wrong hooves. Which Sombra's horn still might, I admit.

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Thing is, the energy didn't evaporate or something: it boiled out of Rarity, then flew away!