Nopony realized that Fluttershy was becoming more batlike again. Well, Fluttershy noticed, and Discord noticed. And apparently Pinkiepie noticed, but decided that Fluttershy was keeping it a secret for a reason, and it would be fun to play a 'keeping a secret' game with Discord. It wasn't until Fluttershy began stealing apples again, and opting to stay inside on even the nicest, sunniest day that her friends noticed. The bat wings had something to do with it, as well. It was probably the fact that Fluttershy had retained her mind this time and not turned into a fruit-sucking sociopathic monster that everypony had thought she was doing fine till there was really nothing anypony could do.
“What were you thinking?! Keeping it to yourself like that! How stupid could you be Fluttershy?!” Rainbow Dash berated her friend as the shy pony cowered, fluffy ears pressed flat against her head and big, slitted eyes wide and terrified. They kept shifting between wine red and her usual spring green, and while Twilight had tentatively put out the idea that it was a sign that maybe this was still reversible, she was largely ignored. “I...um...didn't want to be a bother...” Fluttershy managed to squeak out as Rainbow Dash paused for breath. The rainbow maned pony was long-winded, but even she had to stop for breath every now and then. Rarity sighed and stepped in. “Really dear! It's not a bother when a friend is in need! You could have said something and Twilight would have fixed you before, just like she did the first time! Right, Twilight? Twilight?”
The purple alicorn just put her ears back and chewed on her lip before smiling guiltily and nodding. “Exactly! I would have! No matter what” Except, if it hadn't really gone away the first time, it meant she hadn't fixed her friend but had prolonged the inevitable. So much for the element of magic, she'd hurt Fluttershy more than helped her.
-
It took six months and a very unhelpful Discord (“Have you tried hanging her by her ears? And no, I can't reverse this. I already tried but apparently turning a shy pegasus into a fruit-obsessed bat pony is about as chaotic and random as you can get. I make things random, I can't necessarily turn them back. Really you should have guessed by now!”) for Twilight to admit defeat and turn to the Two Sister's castle for information on the first bat ponies, because obviously they were the only answer. The only thing she could find was that the bat ponies were creatures that had, according to legend, crawled out of the deepest pits of the oldest mountains, and unlike normal ponies, only came out during the night. They were also largely peaceful and quiet creatures, though there was a small passage on their fighting prowess when cornered. They were also, according to the book, capable of dreamwalking like Luna. And many of them seemed to be good with animals. Or, at least good with bats. But there was nothing on how they were created, or what mountain or realm they came from. Besides that book, they also filled tombs of foal stories, how they were the carriers of souls, they helped Cerberus guard Tarterus and they took care of the prisoners there. There were stories of them stealing foals to use as slaves in their towns, but Twilight doubted that much of these stories were true.
Still, it gave her an idea of some of what to expect with Fluttershy, and where to go on any information on how to hopefully reverse whatever Twilight had done to her friend. “Come on, Fluttershy! You don't have to hide under the seat you know” The yellow pony in mention, with a large cloak covering her from hoof to nose tip, stopped shaking under the train bench with her hooves over her head long enough to answer. “Oh, but I do. I really, really do” Twilight sighed. Apparently (or maybe not as Fluttershy wasn't technically a real Bat Pony) the light wouldn't turn them to dust like Pinkie Pie had been screeching for several minutes that it would. This had frightened Fluttershy to the point she'd locked herself in her closet so that she wouldn't have to have the light touch her. But, when Discord had finally listened to Twilight and poofed Fluttershy out of the closet and into the sunlit living-room of a very annoyed and on edge Applejack, she'd only reacted with pain for her eyes and such, and did not explode into flames in front of her friends. Twilight hadn't thought she would, but still breathed a sigh of relief when she was proven right.
The whole train-ride was like that, filled with a quaking Fluttershy and Twilight Sparkle unable to help her. It didn't matter that she was a Princess now. Or the living embodiment of the element of magic, there was nothing she could do to to save Fluttershy from what she'd become.
There was some hesitation to let them into the castle, well, just Fluttershy. The guards suspected it to be Tirek again, and Twilight had to have a more and more embarrassed Fluttershy flick the hood up each time. Finally, they reached Luna's private hearing room, though Twilight had to literally levitate Fluttershy through the doors when Luna said they could enter (at least her Royal Canterlot whatever voice was coming in good use this way) and see her.
Her room was impressive, with tasteful blues and purples and her moon insignia on the throne and the tapestries around her. She smiled at Twilight and nodded. “Princess Twilight, it is good to see you!” Twilight gave her a strained smile as Fluttershy hid behind her. “Yea...good to see you too Luna. Um...I've got a small, eensie weensie problem...” Luna gave her an odd looked and then cocked her head and leaned to one side to get a better look at the shape behind Twilight. “I see...What exactly does this 'problem' entail?” Twilight took a deep breath and began twirling her front hooves. “Um, see, well...ImayhaveaccidentallyturnedFluttershyintoabatponyandnowIcan'tturnherback” She got out all in a rush, and gave Luna a sheepish, guilty grin. “Since they're sort of your subjects and stuff, cuz you're in charge of the night, I figured you could turn her back. Or something”
Luna looked a bit shellshocked with the rush of information, and a bit surprised at the information given. She sighed and magically closed her curtains before getting off her throne and walking to where Fluttershy was behind Twilight. “It is alright, Fluttershy. I do not wish to hurt you, but to help you” eventually Fluttershy was coaxed out of her cloak and stood in the dim light in all her glory as a bat pony. Luna placed a gentle hoof on her head. “I am sorry, there is no reversal. You could give her the appearance for a short time, but she will always revert to what she is now. I am very sorry” Fluttershy's eyes filled with tears and Twilight hung her head in shame. Magic should never be an answer to things, she knew that. But she'd ignored it and look at Fluttershy now.
“However, there are ways to live with it” Came the gentle voice of the Princes of the Night. “What do you eat now, Fluttershy? Mainly?” The pink-maned pony swallowed, her tufted ears drooping as she stared at the floor. “Um...apples. Mostly apples. And other fruit, but I like apples best” Luna nodded and took the cloak, covering Fluttershy lovingly with it. “I see. I know how to help you best now. You can both go home now” Twilight stepped forward. “Wait, if you know how to help her, why don't you do it now?”
Luna gave her a look and Twilight saw the older princess wasn't exactly pleased with her at the moment. Of course she had good reason but still... “Because the mayor of Hollow Shades does things at his own time, and if you want my help you must accept his” she bowed for them, indicating they should leave.
Their meeting was over.