If I put a Charizard GX in play using Ho Oh GX's "Eternal Flame GX" attack, and my opponent evolves into Porygon-Z and uses its "Initialize" Ability, does Charizard GX go back into my hand?
No. Charizard GX is in play as an "unevolved Pokemon" and so is not affected by the Ability.
Source: Burning Shadows FAQ (2017-07-20), TPCi Rules Team (2017-08-03)