Answer 1

Nope, Fly is still an HM move, and even though it learns Fly through levelup, it will still need a Move Deleter to get rid of it.

Same goes with 5th Gen Seel, who learns Dive through levelup.

Comments

Thats pretty stupid. Why learn a move that must be forced to delete by a move deleter?

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It is weird, but any HMs you learn cannot be overwritten normally because you could get stuck somewhere!