I am looking for a movie that I saw when I was a kid (probably about 15 years ago). It was about a boy who was living with extended family (for what reason I don't remember) but he sad and didn't like it. He was picked on and left out of fun things. Somehow he ends up in another land and finds another boy (who lives in that land) and they have flutes that they can contact each other with. For some reason the children in this land are not safe and are disappearing. So the two boys go on a quest to find this children. In a forest they meet this lonely woman who had her daughter stolen. The main character comes to a castle and an evil man lives there. The boy destroys the man and the children come back. The castle crumbles. Also there is a long scene with a well. Also these flutes look like the ones from Peru with different lengths of wood tied together like this ||||
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Any ideas?

This sounds quite a bit like "The Land of Faraway".
The main character finds out he's a prince who has to defeat the evil knight Kato to regain all the stolen children. Most of them he turned into bats if they didn't do his evil deeds. The part with the well is it's a whispering well that tells of the prophecy of a child of royal blood and his companion, riding a white horse, and vanquishing the evil knight.
It's one of my favorite movies! Hope this helps!

I think that might be it. Thank You so much!

You're very welcome! :)