Now, with Barry trying to prevent a death from happening in the future, and generally facing an unkillable god of speed, it makes sense for BF to appear on The Flash, right? Then, who else?
And, as we know, Thawne now exists alive in a timeline, where he was not supposed to exist. The Speed Force protected him as a bunker. But now it made a paradox in itself. The Black Flash is one way to kill such a living paradox, restoring his death to the timeline.
I suspect that the Black Flash will be this "deadline" that affects Thawne's machinations and callous behavior in regards to the timeline (like killing Rex Tyler preemptively, after being thwarted by him in previous versions of the timeline).