What I am about to say might be a bit confusing as it is hard to say.
I have a theory that the Eobard Thawne (Harrison Wells) from season 1 is alive but there is more too it than that.
I believe that When Thawne told Barry his plan on erasing the Flash that he didn't realise that he isn't from an alternate timeline.
When Thawne discovered the Flash's identity, he travelled back in time to erase the Flash from existince, but he didn't know that Barry's mother had already been murdered (This is in the universe that Eobard was originally in) so in murdering Nora, Thawne created the future he tried to erase so he created the flash according to the timeline he knows. (If this was otherwise then in changing the past of his universe, he would change the person he was and this would create a paradox).
When he killed Harrison Wells, he said that he and Tess Morgan created the particle accelerator in the year 2020, this could be a misconception as Eobard will be born in 135 and so in 160 years he will make his journey into the past. He may have got this wrong because after 1 and a 1/2 centuries, history becomes a game of chinese whispers.
When Eobard tries to murder Barry as a child, he is prevented by Barry from the future. This version of Barry is the Season 2 Barry that I believe we will see tomorrow and this would explain how future Barry knew that Season 1 Final Barry was in the other room and tells him not to save Nora.
At the end of Season 1 when Eddie commits suicide, why was Eobard erased from the timeline as he was not born in this timeline (He travelled here from another timeline) because no matter what anyone on this Earth does. Eobard was still born in another timeline (Apparently). The only explanation for this is that Eobard was from this timeline and just had his facts wrong.
Now for any of this to make sense as to why Eobard appears in tomorrow's episode and why the paradox's don't destroy the universe (Or whatever paradox's do) Eobard in some form has to be born or he has to not have really been erased. Since he now CAN'T be born, this means he wasn't truly erased.
How is this possible??????
When Eddie commited suicide, Eobard was but a version of him AFTER being erased, goes and impregnates his great-great-great grandmother to ensure his existence. But because this didn't happen in the original timeline (Despite the Timey-Wimey aspect) Eobard didn't become his own ancestor until he travelled through time to make it so. At this point, the Eobard who had just been erased, gets reformed into his harrison wells face and then goes through time to impregnate his great-great-great grandmother to re-exist himself and so-on.
If this is true and the original timeline remains intact, then Barry is DESTINED to marry Iris, he will be promoted in the CCPD, he will form the Justice League and create Gideon.
Tomorrow's episode should be Thawne's origin story (Hopefully)
If anyone has any questions or comments, please feel free to leave a comment. :D