Well, even if they did, it'd be because they killed him off on Flash Season 1 and restoring him to that. That said, I have NO doubt that Thawne will return, at least once a year, to the Flash.

I strongly suspect that he's as alive as he ever was, post-Flash Season 1. We'll see him again for sure… comics-wise, he came back from worse than this multiple times. Heck, he came back from this SPECIFICALLY right before he tried to kill the bride at Barry's 2nd wedding.

It'd be completely in-character for Thawne to have travelled back in time to develop a color additive used in all sodas that triggers Barry and ONLY Barry to develop urination problems. He's THAT guy.
Part of the reason that Barry's Rogues are so great is that John Broome and co. intentionally set out to make them all…

Trying to work out the Flash dynasty was ridiculous BEFORE we had to factor in Barry's evil twin…

Immortus is an entirely different barrel of fish, especially since he manages to become his own independent entity in Avengers Forever. (And is VERY angry when he's forced back into Kangdom in Earth X…)

I wrote it in it, too. :)

To say the least. Oddly, Barry's kids marry into Thawne's family. Thawne doesn't take it well.

Just the tip of the iceberg with Thawne. His WORST actions aren't even in that list… and, horrifically, he still may not be the worst person in his family line.

Not gonna lie, I was really hoping Jemma would be a Deathlok in this episode, as a shout-out to the comics.

In the Marvel Universe, they prefer Zuvembie. :)

Kang's smart enough to never alter his own timeline. :)

As soon as Malcolm rebuilds Thawne's time machine and goes and resurrects him with the Lazarus Pit of a previous era…

Or we'll see them do so IN LEGENDS, thus requiring nothing odd in their own shows.

I'd love to see the Demon Knights in an episode at some point. Well, minus Savage…

Turns out, he likes money. :)

Or even just a jerk Booster Gold… especially if he shows up with Rip in tow…

He's DC's scariest villain. Yes, worse than Darkseid or the Joker, in that he's ridiculously powerful AND enormously petty. This is a man who changed his own timeline in order to eliminate his sibling because an only child would have more resources. He pushed Barry down a flight of stairs when he was six for no reason…

I find myself wondering if he had Grodd as a backup plan to ensure his survival.

Plus, nobody EVER promised that Thawne was a one-universe phenomena… he probably exists in all timelines, and, in theory, still might have bodyjacked some random individual from THIS timeline in a blink of an eye as well.

The Speed Force would have killed Barry long ago if it hadn't have been for needing him to balance out Thawne. :)