User blog comment:TheDoctor230/Eobard Thawne Alive?/@comment-107.142.37.58-20160201004715

When Eddie killed himself, it should have erased Eobard Thawne from existence. However, a past version of Eobard Thawne was inside the speed force time traveling, so he wasn't erased from the timeline. That's why he's called a timeline remnant in the episode. Basically, by Eddie killing himself, it erases Eobard from existence in that moment, but a past version of him still exists. That past version of him goes on to usurp Harrison Well's identity and create the Flash. That's why deleting Eobard didn't also delete the Flash. It makes a lot more sense than the explanation we were left with last season, if you think about it.