4 years on, and this just happened to me in Unreal 4.21.
I just followed a simple tutorial for the open world asset that ships with the game to set up a rock layer and a grass layer.
It worked last week, and this week when I go to pain, I get a black square. Pressing undo gives me an even larger black square.
The layer order as mentioned above did not matter, and “build geometry” did not matter either.