Midnight Sparkle still exists inside Twilight Sparkle but not a representation of Twilight's darker side but was instead her other half, the half that had the power she was meant to have, obtaining the geode was the first step in accepting that power but was not time but since they're facing whatever villain that's up to the writer who'll pick it up the time has come to accept it but not without a permanent appearance change and here's my version of the scene.

Twilight Sparkle was in her mindscape believing she was alone until she heard a familiar voice, that of Midnight Sparkle “You and your friends are going to fail you know.”

“I don’t believe that, we’ll still prevail and how can you still exist?”

“Not without help, I’ve always been apart of you since the games but after thinking for a time since Camp Everfree I came to realize what I am among other things.”

“And what’s that?”

“That I’m that half that contains the power you’re meant to have, that magic already existed in this world but it hasn’t been used for sometime.

“What do you mean by the half that contains the power I was meant to have?”

“Haven’t you felt the changes to you since gaining that geode?”

“Yes.”

“Gaining that was the first step, my appearance at the games showed you weren’t ready for that power which you now are ready, you just have to let me return it to you.”

“But what will happen when I do?” Twilight asked a little scared.

“Only one way to find out but know this there’s no going back. So will you accept it back despite that fact? ” Midnight responded while holding out a hand.

“I accept it back.” she replied reluctantly but after she grabbed the hand Midnight spoke as a white light engulfed them.

“Oh one last thing there may be some changes that’ll be permanent.”

“What do you mean?” Twilight asked her other half who spoke for the final time

“You’ll see.”

“Do you think we can still win this Sunset?” asked Rainbow Dash while grunting in pain.

“We can still win.” she replied in pain as well but before the conversation could go further Pinkie spoke.

“Something’s happening to Twilight!” she said while noticing a glow engulfed their friend which gained the attention of everyone there before the light went away revealing Twilight had changed into a winged figure the six friends had hoped stopped existing after Everfree but before they could say something the figure put a shield up and turned her head towards her friends.

“Don’t worry girls I’m still me, now you rest and I’ll take care of the rest” she said with a reassuring smile before turning her attention back to their foe.

(Later after their foe was defeated)

“How is this possible and are you able to change back?” Sunset asked her friend.

“I believe so let me try and find out.” her friend responded before closing her eyes in concentration for a few seconds only for nothing to happen “Well I guess this is one of those permanent changes she said I’d have.” she finished as she looked at her changes.

“You mean you’re stuck like this?” the light amber girl asked worryingly.

“Maybe not, let me try something else.” her friend responded closing her eyes once more in concentration before her form changed back into what she once looked like with her wings disappearing. “Well at least I can hide what I really am now.” she said satisfied at the result before speaking once more “Could you hold my geode so I can try something real quick?” she asked holding out her geode which her friend complied and after that she started using magic before having her friend return the geode. “So she was right in that there’s magic in this world and it was only dormant.”

“If there was magic in this world then how come your device didn’t pick it up despite it being dormant?”

“I guess it was because it was dormant for so long that no instrument could pick it up.”