User blog comment:Starcitiesfinest4/Reverse Flash/@comment-3221148-20161107084321

Time remnants. The current, prime Eobard never became Wellsobard, never had Wells's memories, knowing only what Barry told him of that time. By traveling through the Speed Force from 2000 to 2016, it protected him from the grandfather paradox of Eddie dying. For the memories of timeline, both Eobard's (original timeline before he traveled to 2000) and Barry's (altered timeline after 2000) to make sense, a Wellsobard had to exist, even if it wasn't the current, still-alive Eobard. The dissipating body of a previous Eobard might be confusing here, so aasume this: retroactive time remnants. As in, for Barry's story so far to make sense (and not disappear, like it started to do in Flashpoint), a time remnant Eobard-Wells somehow appeared out of the Speed Force, before getting erased by Eddie.

Now we have the Pre-Season-1 Eobard living in the world where Thawnes are erased from existence.