It was my understanding, and from past experience, that the move "Swift" was the only move that could hit you when using "Fly". Kind of like Earthquake being able to hit me when using Dig. But I was recently playing Heart Gold and I was taken out with Thunder when I was flying.
So what all moves can hit you when using Fly? And did the types of moves that can hit you change throughout the different generations?
Best Answer
Yes, the moves that can hit you have changed over time:
Presumably, the Generation I list was actually a bug which caused the "semi-invulnerable" check to get skipped (with Bide getting fixed for Stadium); the list used for Generation II and on were selected because it makes sense that these moves can still hit while the opponent is flying.