My current crazy theory that is likely to be completely wrong is as follows.
Wells went back in time to kill adult Barry, not child Barry. He succeeded in killing adult Barry, which is why adult Barry vanishes in the middle of whatever crisis is shown on Wells' future computer. Killing Barry causes the speedforce to become too weak to allow Wells to travel back to the future, stranding him, so he has to create the Flash and help develop young Barry into strengthening the speedforce again so that there is enough of it to allow him to travel back to his own time.
Which happens. Possibly not by killing Barry, but Wells gets back to his own future. Which is now a horrible mess because the Flash was instrumental to stopping aforementioned crisis. So now Wells has to come back and save Barry from himself, somehow.
This theory is largely based around the fact that I desperately want Tom Cavanagh to stay on the show.