She sang too much, to the point of abusing and damaging her vocal cords.
Her official profile on Sony Music Entertainment Japan mentioned this
15歳の頃、歌唱による喉の酷使が原因で、突如声が出なくなるアクシデントに見舞われる。
At the age of 15, she underwent a sudden voice loss accident due to overusing her throat from singing.
This was also mentioned in her interview with natalie music (Japanese)
──「15歳のころ、喉に異変をきたし」という記述が公式プロフィールにありますが、[...]
── The description "at the age of 15, an accident to the throat happened" is written on the official profile though, [...]
歌の歌いすぎが原因でした。[...]
The cause was too much singing.
However, more detail was in her interview with BARKS (Japanese) about her 1st album, "Sleepless Nights", especially on the song "夜行列車~nothing to lose~" (Yakou Ressha-, Night Train-)
――で、今回、これまでのシングル曲全曲に加えて、新曲が3曲入っていますけど、「夜行列車~nothing to lose~」は、Aimerさんのアーティストとしての出発点を感じさせる内容になってますよね。これは実話?
――Then, this time, in addition to the inclusion of all the singles until now, there were 3 new songs, but the substance in "Yakou Ressha~nothing to lose~" feels like the starting point for Aimer as an artist. Is this a true story?
Aimer:基本的に歌詞は、自分の体験もちりばめながら一つの物語を書くようなイメージで書いています。なので、この曲もそういう感じですね。
Aimer: Basically, I wrote the lyric that includes my experience, with an image to write a single story. Therefore, this song is also like that.
――“さよなら 夜の教室/ここで私は声を失した”というフレーズがとても印象的でした。
―― The phrase "goodbye night classroom / here I lost my voice" was very impressive.
Aimer:ああ……声が出なくなってしまったというのは実体験なんです。私は常に音楽が流れているような家で育って、物心つく前から歌うのが好きな子供で、気づいたら歌手になりたいと思っていたんですね。で、いつも一人で歌っていたんですけど。15歳の時、朝起きたら突然声が出なくなっていたんです。それで、声帯を診る専門の耳鼻咽喉科に行ったら「とにかくしゃべらないでください」って、沈黙療法というのを勧められて、そこから半年間ずっとしゃべらずにいて……。
Aimer: Ah... the voice loss was a real experience. Because I was grown up in a family that constantly playing songs, being a kid who likes singing before reaching the age of discretion, and when I realized, I thought I wanted to be a singer. I was always singing alone, though. At the age of 15, when I woke up in the morning, I suddenly lost my voice. After that, when visiting vocal cords specialist in a department of otorhinolaryngology (ear, nose, and throat), they said "in any case, please don't speak" and recommending a silent treatment, since then I didn't speak for 6 months at all...