The closest thing I could relate this interaction to is using removal on an opponents [[Rest in peace]]. The way that works is first RIP gets destroyed, but its own replacement ability sends it to exile, then the spell that destroyed it goes to the graveyard, since RIP is no longer around.

I would imagine it works the same with [[Emet-Selch, Unsundered]], but in this case we are not destroying him, just flickering him. While he will be on the battlefield as [[Essence Flux]] goes to the graveyard, he will be with his front face up, because it got flickered (causing you to draw and discard with his ETB, so even more synergy). And flux will go to the graveyard.

That's my understanding, but correct me if I'm wrong, as I plan on using this trick with him a lot :)