I'd add detail to the character/story/their change arc that is scary (for the writer and reader) and that hurt the character.

A touch of sadism is never a bad thing when it comes to your characters... :D

In essence, go deeper!

Some suggestions:

Emotional wounds and ADHD

Give her an emotional wound. Maybe she's suffering from ADHD (which would translate to a learning disability and social difficulties).

This energy bundle you describe may have a dark side.

A quote from your TV-Trope link:

a good way of telling whether a female character is genki or not is to see if her family and peers are exhausted, astonished, or even creeped out by her chronic outbursts of vitality.

I.e. social difficulties. Maybe family members will put up with her but will strangers? Friends? Possible boyfriends?

This type of person will also go bonkers when supposed to sit down in school and understand stuff that doesn't come naturally (learning disabilities).

Anger management issues could also result from all that energy. It could turn dark and hateful (especially if/when the hyperactivity is not received in the best way by the surrounding and it's still pumping in her head... because, no, with ADHD it's not impossible to turn it off, it just takes years of training and a magical mixture of discipline, age, and acceptance to do it... before then, you're it's bitch and the rollercoaster keeps spinning...)

With ADHD it's also usually the case that while a person is hyperactive, they don't have hyper batteries so there will be this energy bipolarity where they swing from high energy to exhaustion (and as day turns into night even flat out falling asleep standing). Unless something happens and the activation explodes again and there's another hour of wide awakeness... three o'clock in the morning. (And then, of course, sans hyper batteries... count on a very bad morning... until there's another kick of ADHD and things start spinning... Saturday's favorite past time: catching up on lost sleep).

Other effects of deflating could be even harder to concentrate (did I mention people with ADHD concentrates... on 1001 things at the same time?), get irritable especially from sleep deprivation, or even self-medication (using alcohol to fall asleep or any kind of energy pills to get out of bed... at first) and in the long run, depression.

If you do choose to give her ADHD, it's a disability which means she needs to be disabled somehow. Some parts of her life don't work, or only work with more than average effort from her and the people around her.

Double-whammy: ADHD+Autism

The TV-trope definition of the genki-girl mentions a person that isn't that good at picking up cues that her behavior is making people "exhausted, astonished, or even creeped out".

Maybe she's not just suffering from ADHD but also autism?

This would make her a bit less energetic, but it would also make her clueless to the fact that people will dislike her energy outbursts at times.

She could become a very confident, but lonely person that everyone else is having a hard time understanding.

It's also possible that autism makes her less inclined to really feel alone, so the combination of autism and ADHD makes her a very strange creature. A kind of shallow cocktail-party-person that talks about the deepest subjects but never returns any phone calls or form any lasting friendship bonds. (After all, she has her one or two best friends... do you really need more?)

Deepen the change arc

Or, if you don't want to add a disability or emotional wound, you can deepen the character in other ways.

You're right about the change arc. I don't know which one it is (but here's a good resource for different change arcs).

Here too, you go deeper. Maybe the truth and lies portrayed in the arc are too trivial? Can they be about life and death? There are several types of death to choose among. James Scott Bell mentions physical, psychological, and professional death (also see here).

If the character follows a flat/testing arc (she will believe in a truth in the beginning and in the end). She will get tested and go through trials for her truth. Everyone, it will seem, will want her to stop believing in it, and it may be necessary for her to sacrifice everything (even her life?) for that truth. Regardless, she will pay dearly for having the audacity to believe in such an outrageous truth.

You can increase the cost of abandoning the truth or lie in all the other arcs to eleven in just the same way. Make. It. Hurt. ;)

Wants and needs

Also, look into what the character wants (her goals) and what she needs. Make it hurt to give up what she wants. Make her scream and struggle to get it... maybe she can have both what she wants and what she needs (which of course should never be the case—they should be mutually exclusive!)

"I'd rather die than give up what I want!"

"You will die if you don't give up what you want!"

"Arrgh!"