Hey there - loving the course.
I am using version 2.78c and when I used the difference operation to take the notch out of the bishop there were no faces to the inside of the notch. I selected all the vertices and added faces to the geometry but it did not look like that was needed in the tutorial video.
In this updated version, it seems that there is a field that was not shown called solver with either BMesh or Carve - maybe this is the reason? I could see that having to go back and add the faces back in in a complex geometry would be either challenging or a time-suck.
Any assistance on what I did differently would be greatly appreciate.
Here is a pic of first pass after filling in the faces in the difference cut.