Hey everyone! I think it's going to be a little hard for me to find the anime I'm looking for because I was 5-6 years old when I was watching it and I don't remember lots of it.Back to 1990-1991 , the story is about a girl that fights in a war and at the end something really cool happens and she get lifted by something that looks like huge worms and she somehow transforms to a boy and there are some villagers around her-him that are initially scared but after that, they are really thankfull because the war ends.Don't remember much more.. Anyway, I hope tha I find it because it was amazing! Bye

Part of that sounds like it could be Nausicaa of the Valley of the Wind, but she doesn't turn into a boy.
http://www.originalsoundversion.com/wp-content/uploads/2008/06/june-2008-31.jpg

I never wanted to watch it, but if a girl transformed into a boy, it sounds like Ranma 1/2. Though there I don't recall that anime having anything to do with a war.