Well, seeing as you said that this happened after you updated it, I do know your problem, and it’s not something you can fix. In the update, as seen with your picture an my 4.0.0 non-updated version, they changed how many layers there are. So, instead of you having: ground, mask 1, mask 2, fringe 1, fringe 2; you have: ground, mask, fringe. This took away those black/blank layers that you are seeing on your screen. In short, it just deleted all of those layers that you had in mask 2 and fringe 2 when you updated. So, all you can do now is just fill it in the best you can and hope that the team puts the other layers back in. I hope this answers your question entirely.
P.S. This code is in the sever so you cannot edit it to make more layers, hence I said you can do nothing about it.