Cannot use fly when being teleported to different part of same game

This is just someothing that has been bugging me for a while. When i get teleported to a differnt section of a game after i needed fly for the first part of a puzzle of some sort, i cant use it again hen i get teleported. I don't know if there is a way fo fix this or if i just have to deal with it. If you know a way to fix this that would be appreciated.