From an article in MaxPreps from Feb 2010, Flatt talks about the original injury to her back:I thought Flatt did.

Flatt crowned No. 1 female figure skater in U.S.
MaxPreps News - Not even two bulging discs have kept 17-year-old Olympic hopeful Rachael Flatt, a senior at Cheyenne Mountain (Colorado Springs, Colo.), from reaching the pinnacle of American figure skating.

"When she was 13, Flatt came out of a spin, fell and injured her back. The bulging discs have been with her ever since. She has been able to at least partially overcome the problem, but it lingers." ( The initial injury took place before her first JGP assignment, which was to be in Mexico City, but she had to w/d and ended up going thru the Q system to get to US Natls that year....her Jr US season.)
and a more recent Stanford article....she has 3 ruptured discs in her back:

Former figure skating champion Rachael Flatt on coming back after injury
Like many Stanford students, Rachael Flatt '15 doesn’t know what her future holds. But unlike most of her peers, she is not attempting to figure out her first

"Before graduating from high school, Flatt won the 2010 U.S. National Figure Skating Championship and skated to seventh at the Winter Olympics in Vancouver. A year later, Flatt enrolled at Stanford, intending to pursue a degree while continuing to compete professionally.
Since 2011, however, injuries have taken their toll. Last summer, Flatt re-aggravated three bulging discs in her back, and developed tendonitis in her ankles after returning to training. In October, Flatt was forced to withdraw from the rest of the 2012-13 competition circuit to give herself time to heal. She only recently began training again for an exhibition show in February"
Skating is tough on these kids. No doubt about it. She only really talked about her back issues at the end of her career, but it was apparent after her novice season she could no longer do the amazing laybacks she had as a 12 yo. Hard to believe Flatt incurred the first ruptured discs when she was just 13, and managed to continue to skate, acquire 3x3 combos, win the world jr championship, US Nationals and go to the 2010 Olys. But the years of back and lower leg injuries took their toll for sure.
Skaters are tough. I don't many people fully appreciate how banged up they are by the time they retire.
And, you look at what her peer group has gone thru....Mirai has had several surgeries (hip flexor IIRC), and Caroline Zhang's back surgery. Wagner, to the best of my knowledge, is the only one who did not endure chronic injury issues.