How does Vanishing Rasengan work? Vanishing Rasengan is a miniature Rasengan which was originally developed by Boruto as seen in Boruto: Naruto the Movie. In that movie, when Boruto was trying to learn Rasengan in front of Sasuke, it was observed that his Rasengan usually vanishes into the air but the effect of Rasengan is still there.

How was Boruto able to make the Rasengan vanish? How does Vanishing Rasengan work?
As wiki said, Boruto create a miniature of Rasengan then he inject the Rasengan with Wind release nature, so the it can be thrown.


  The user creates a miniature Rasengan, to the size of a big grape,
  which is capable of being thrown due to the Wind Release nature
  transformation that is applied. While gliding in the air, the sphere
  disappears and hits the target.


About your question how Boruto was able to vanish the Rasengan, I think because it's so small, slowly vanishing while thrown but still hits the target because his Wind Release nature. But it's only my opinion of course.