With the mid season premiere of The Flash, there are plenty of questions worth raising: what's Harry up to? Is this the end of Barry and Patty? Will Jay ever get his speed back? But I think the biggest question this week is: how is the Reverse Flash alive?
Now I think it's safe to assume that we are all aware that this is not the Thawne we know. This Thawne has never met Barry as far as we know. This is the Eobard who has traveled back in time completely by accident. But this raises a very big question: if Eddie Thawne died before planting his seed and continuing his legacy, how is this younger Reverse Flash here? The boring answer (and wrong one) is that Eddie must've had family. If this was true, our old Harrison Wells lookalike wouldn't have vanished in a brilliant Flash of light.
Here's the thing, when Eddie killed himself, it wiped the timeline of all things Thawne after that point. Eobard Thawne never existed. However, somewhere outside of time itself, Eobard Thawne was running at superspeed, traveling back in time to the year 2016. Being outside of time, this Eobard Thawne was completely unaffected by his nonexistence.
Why didn't Thawne vanish upon arriving in 2016?
This can be answered by looking at the season one finale. When Eddie sacrificed himself and erased Reverse Flash he managed to create a grand old paradox, which our heroes named the Singularity. This black hole was supposed to erase the entire timeline. There was no reason for it to exist, its mere existence is against every law of nature there is.
The man who murdered Barry's mother never existed. If he were to travel back in time to the night she was murdered he would find her alive and well getting ready for bed. When he managed to find his way back to 2016 it would be a drastically different world. It would be very much like Justice League Flashpoint. Also, think of the Back to the Future scene where Doc Brown explains the alternate 1985's.
This singularity should have erased the current timeline, but Barry, with the help of Firestorm, managed to close the hole, successfully saving this timeline. But, because this timeline has no reason to exist, the Reverse Flash was able to slip into this universe without time correcting itself by erasing him. And so the Reverse Flash loop begins anew, where he shall battle with the Flash, travel back in time to kill Nora, get trapped there while Barry makes his getaway, and then wait until the time comes to begin his dastardly plan for vengeance.
Chances are they'll find a way to explain Thawne's return far better than I could ever hope to, but this is my theory. Thanks for reading!