Board Thread:DC's Legends of Tomorrow discussions/@comment-24856931-20161028033138/@comment-3423279-20161028065205

Or, another theory is that Eobard appeared in 2016 but didn't encounter The Flash as he didn't have his powers yet and just left, killing Tina after she made his time portal.

That, or Reverse-Flash's time jump was moved by the Speed Force to ensure the slightly altered timeline happened roughly the same as before.