Question

I've seen conflicting information for this - some say these two moves do double damage if a pokemon is in the air from Bounce, some say regular damage. Which is right?

Answer 1

As of Gen 3, Thunder (but not Stone Edge) can do double damage against Bouncing Pokemon.

Comments

OK, and Stone Edge can definitely hit them during Fly?

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I have tested this myself and Stone Edge definitely does not hit pokemon during Fly or Bounce.

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Sorry, I was going to also put in that it can't hit them, but I forgot.