This is a really good story! Interesting, intriguing. You have a point to each scene so that not one seems redundant (except maybe for the one they both meet - but I'll come back to that) and I really really love the theme of this. It reminds me a
little bit of "The Royal Doll Orchestra" because of the mysterious atmosphere - they just both give me similar vibes. And I love that manga

(and I love music, since I have played the piano for, oh hells, already 12 years!).
What you
could improve is description. Description of the surroundings, sounds, smells. You could add a bit of description here and there (but don't go overboard xD). It's just that I can't get a good image of the place, of their world. Maybe try to picture the place in your head as detailed as possible, and then put in bits and pieces of what you see, hear, smell and touch (how surfaces feel, or the humidity or heat or cold).
Regarding the scene where they first meet again: this is the only scene that to me seems a bit redundant. Why do they meet before school? Is it important? Is the point of the scene that Violan hums the tune Altona has stuck in her head so that she somehow recognizes him a little? If so, you could try to make it more important in that scene, make it the main point. Maybe by making Violan hum the tune before he speaks to Altona so that she pays attention to him before they actually meet, and make Altona wonder about that tune from start to finish.
That's just an example, though, and I don't want to tell you how to write your own story, since you're the only one who can write it (or else, it wouldn't be
your story). =)
You could use a betareader. I have spotted several typos and missing comas and such. If you want me to look it all over and correct it, I'd be glad to help!
So, now you have another reader because I'll definitely keep an eye at this story ^^
(I saw your story on the Inklings topic, so, hello, fellow writer!)