Most fans of the CW Series The Flash were left scratching their heads after the Season One Finale, but don't worry; There is a plausible explanation for everything.
OBVIOUS SPOILERS BELOW
In the finale, Detective Eddie Thawne bravely sacrificed himself in order to destroy the existence of his future evil descendant. (And conveniently clearing the path for Barry and Iris' future relationship). So where does that leave the events that created our hero? Without the Reverse Flash's plotting and subsequent efforts, none of this would have come to be.
The answer, my friends, came popping out of the space time portal in the form of a polished silver and gold helmet. With the arrival of the WWII Flash's helmet, we now have not only time travel, but dimensional travel as well.
The original Flash, Jay Garrick, comes from another Earth; Earth-2 to be precise. Even with the events of the finale, we can still have the influence of the Reverse Flash from Earth-2. (I'm sure he has it in for Barry no matter where Barry exists.)
With this revelation, Tom Cavanagh can exist again as the REAL Harrison Wells. - with his beloved wife resurrected to help inspire the creation of S.T.A.R. Labs. The Reverse Flash from Earth-2 can pop in from time to time to cause the chaos we've come to expect (INCLUDING alternate events that created our heroes and some of the Flash's rogue headaches).
With all the time paradox stuff swept out of the way thanks to parallel dimensional influences, Season 2 should be an exciting trip for us all!