It is entirely possible that the method of release is somehow 'breaking' the link between the Pokemon and the pokeball, as this situation would indicate. It doesn't contradict the overarching idea that so long as a Pokemon is 'owned', it is tied to a given pokeball, and others would therefore fail against it (excusing situations like the balls in Mewtwo Strikes Back, which by design circumvent that).
In Greninja's case, wasn't there a scene showing that Ash still had its pokeball? In any event, I don't think Greninja is any more released than Charizard was; it's just not in a fixed location to be called upon from. It was ceremonially released, but it is still owned by Ash and in theory could reunite with and rejoin him.
Something else that strikes me is what if the trainer loses their pokemon's pokeball? Which I mean, wouldn't be uncommon.