Nobody said Eobard Thawne was directly descended from Eddie.
[SPOILER ALERTS for those who haven't seen Flash Episode 123 yet] (...and why haven't you?)
This is my first crack at one of these things, & I don't have a heck of a lot to say, but here I go.
In the season finale of The Flash, while everything is insanely out of control, Eddie Thawne shoots himself, ostensibly stopping Eobard Thawne/Harrison Wells/Reverse Flash from existing.
...or DID it?
1) Is Eobard DIRECTLY DESCENDED from Eddie? In episode 122, Thawne dismisses Eddie as a non-player in the future of the speedsters. I never heard him say "oh, you're my Gramps" (Case in point: I'm related to King Kong screenwriter James Ashmore Creelman, who also committed suicide, but I'm still here.)
2) is Eobard actually dead? Simple solution here: Eddie's death doesn't ERASE Eobard from EXISTENCE, he just erases Eobard from being in THAT LOCATION at THAT TIME! The so-called "Butterfly Effect" could simply mean Eobard made "that left turn at Albuquerque" and just wasn't there at that moment. Given how much of a Chess Player and manipultor Wells/Thawne is, it seems like telling Eddie what he did was actually part of his escape plan!
In which case...
3) All Eddie did was prove he indeed is the non-player Eobard made him out to be. Eobard told Eddie he was just historical flotsam.
4) If we've learned anything from this, it's that we can't trust ANYTHING Eobard says. He has no moral compass. Everything he does is to better his own existence. Given the chance, he'll kill anybody who gets in his way. Maybe he anticipated Eddie's choice and uses it to make his escape. given that the whole world is collapsing for a cliffhanger, it's not impossible to believe that this is all part of Eobard's master plan.
...oh yeah! There's also...
5) We don't even know what happened between episodes 122 and 123. Either Eobard OR Eddie could've figured into that battle in a way that altered the fragile ecosystem of the timeline.
If you think about it, with Thawne and The Flash both able to time travel (with the added throwaway reference to Vandal Savage (see: LEGENDS OF TOMORROW trailer)) it's possible to have the entirety of season one scrapped in a "flash," or replayed over and over. Barry already tweaked the timeline with his own self-rescue. And again when he captured Weather Wizard.
Hang on, my friends:...
This is just the tip of an iceberg bigger than even Captain Cold could conjure.
I, for one, can't wait.
(On a side note: I just made the connection between episode 123, and Silver Age Flash comic book issue #123, which brought Barry face-to-face with Jay Garrick in the FLASH OF TWO WORLDS story. G(on a side note: I just made the connection between episode 123, and comic book issue #123. That book famously brought Barry face-to-face with Jay Garrick in the FLASH OF TWO WORLDS story. Garrick's helmet shows up in the particle accelerator. ...just sayin'...)