Board Thread:Naruto: The Last Discussion/@comment-26010916-20150213211756/@comment-5936871-20150329153849

Well even though Naruto apparently lost his Six Paths Sage Mode in the movie. That was probably due to Toneri extracting all of that orange chakra from him earlier, which was probably the chakra of all the other tailed beasts. So even though he lost their chakra, he still retained Hagoromo's Six Paths Senjutsu which is what probably gave him the ability to fly.