I think you can do this with Yanfly's Buffs and States Core. You could have a "fly" state and a "fly" skill that initiates the state.
Use the <Custom Add Effect> lunatic mode notetag to run a common event that changes the player's graphic to the "fly" graphic and sets through to on. You can also have this common event remove the "fly" skill and add a "land" skill.
Then, use the <Custom Remove Effect> notetag to run another common event which sets the graphic back to the normal graphic, sets through to off, and removes the "land" skill and adds the "fly" skill.
Why don't you try it out and see if it works for you