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While Lock On/Mind Reader will generally cause moves to bypass Fly (and Dig) in GSC, there are some oddities:
* Earthquake/Fissure/Magnitude will still not hit through Fly (however the reverse doesn't apply -- Gust/Twister/etc will still hit underground foes)
* Status moves that bypass accuracy checks but not Fly/Dig will
not do so even when Lock On/Mind Reader is active (Mimic, Mind Reader, Lock On, Curse used by a Ghost, Foresight, Attract, Nightmare, Transform)
* Moves that reduce a foe's stat will not do so if the foe is flying/digging. For moves that has this as primary effect, the move will simply fail and for moves which does this as a secondary effect, the move will just not lower the stat.