The same thing happened with some of the other CW superhero shows last year though it might of been easier to keep those shows running since they're all filmed in Vancover and I'm sure they have a major production base there for the shows (and even with that I remember that a bunch of Supergirl episodes got delayed), I believe Black Lightning films somewhere else.
Supergirl was unrelated to the Kreisberg removal. That itself impacted neither the Flash or Supergirl.
They film in Georgia. BL is also unconnected to the other shows due to Akil's desires(for the best). I would hope it continues and they get another black showrunner with a strong voice to helm.
But hopefully one that wants to integrate to the main universe.