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)

Relevant cards

Note: All applicable cards may not be listed below.
SM3_105
SM3_105A
SM3_105A
SM3_131
SM3_21
SMA_SV50
SMA_SV50