Originally Posted by
linayar
The implication that I get is they weren't erased from existence, only a separate timeline was created. That's why the Exarch remained.
The people, maybe, not the timeline.
That's not how it has to work. In this case, the subversion is in the role of Zodiark, challenging the audience's notion of seeing Zodiark as the source of evil due to the Ascians' deeds, when in truth, Zodiark was a tool from the start, which can be used for good or evil, and can be misused with bad outcome, even to the user.
Nothing actually has to become of Zodiark other than being shown for what he truly is all along. Simply showing his actual role that slightly differs than the people's expectation (but still makes sense) is enough of a subversion. And just because you don't like it doesn't mean it's a misuse.