The process was old and very specific. It could not be forced, it could not be done to a pony who had their cutie mark and the process would create a young queen. So most hives would not have bothered with it in the first place. Fluttershy was willing to set up the pod if Scoot decided to go through with the procedure but it had to be her decision or the pod would just spit her out. She had spoken with the girls about it without revealing what the treatment would be, only that it would be permanent.
Fluttershy had been speaking with her friends (and the Princesses [eep]) and had agreed after some 'gentle' prodding over several weeks and a promise of protection to reveal her true form at the up coming Gala when Midnight and Nightmare revealed their relationship. She was being offered a place as the head of a new noble house due to her being of foreign royalty, which was enough to be considered noble with royal permission.
Now came step one: letting the girls know. "Scootaloo, how much have you told the girls about the treatment?" the girls jumped they had not heard her come in.
"Only a little. Is that okay, mom?" Scootaloo did not want to cause her mother any more panic problems.
Fluttershy smiled "If its okay, I'll explain the procedure to you all."
The girls were sitting in front of her, immediately ready to hear what would happen to their friend. "Now the process she can use is to go through something that is akin to a cocoon for a caterpillar. The procedure will allow her to fly by turning her into a little known type of pony called a Changeling" The girls were speechless for a second.
"How would that help her?" Sweetie bell was the first to speak up.
Fluttershy smiled kindly before erupting in a pink flash revealing her true self "This is what a changeling looks like, girls. We have the ability to fly and cast magic and are able to change our appearance at will to blend in. I hope I don't need to explain why we would need to do that?"
The girls shake their heads but Diamond has a contemplative look "Why are you telling us about this now?" The others look at her for an answer which she happily gives.
"The Princesses have made sure we're included in the anti-discrimination laws when they were updated this year and seeing as I'm technically a Changeling Queen, I can apply for noble status and I'm on record as Princess Nightmare's Beastmaster for the Lunar court.
Apple Bloom had to say something here "Hold on. You mean we have 2 princesses living in Ponyville?" at the same time Diamond was hiding the fact that she was about to pass out from having insulted 2 royals on a regular bases before getting some sense knocked into her.
Fluttershy nodded "Well Scoot will only be an official princess if she decides to go through the change."
Scootaloo interrupted her mother. "I'll do it."-the girls looked at her shocked "The only reason I was worried was because I had no idea what to tell you girls. If I don't have to hide, I have no problems."
Once Shy double checked that yes, Scoot was ready and the girls did not mind staying with her, she set up the pod for Scootaloo and made sure she was comfortable. The girls than spent a lovely evening talking with Scoot through the pod before she fell asleep due to the procedure so the girls finally went to bed to be ready for the next day.
The next morning the girls were woken up by the sound of something cracking. when they looked the pod was shaking then it burst open and Scoot tumbled out.
(By Astrera )
Scoot stood up, rubbing her eyes and without noticing, she started to hover her wings buzzing like crazy. She felt stronger than ever, the love of her friends and family had been feeding her during the transformation as such she was in much better condition than most changelings. She still had her mane. No holes were present anywhere on her body and, with a quick internal check, she was happy to see that she was still producing her own supply of love energy. Just like mom.
That had been surprising to discover the tree had apparently activated the ability to produce proper levels of love in Fluttershy, to remove her greatest weakness and her fear of hurting other ponies when she had to feed. The girls had to run to school with a letters explaining scoot was absent for medical reasons and Scootaloo spent the rest of the day learning how to shift back into her pony form. Fluttershy had a feeling that this was going to take awhile.