I'm having the same problem...
I understand how the Boolean tool(s) works and the importance of the correct order of operation to get a desired shape, but the geometry keeps disappearing on me. The geometry dissapears completely from view, no fragment, nothing. It gets even worse: according to the Outliner, the two objects that I used in the operation (polySurface12 and pCube13) do combine to form a new object (polySurface13), however, the viewports shown nothing except for that X,Y,Z-cursor-thing hovering in mid-space without an object to go along with.
I have had this problem a couple of times before, and the operation seems to fail with certain (complex) geometry. The shape that I want to use to do the cutting away with is a polygon with well over 50 faces to it, and the polygon that I want to cut out of is no less multi-faced...I've created a simple (unedited) cone and tried to Boolean with that...frustratingly enough, that worked fine... :headbang:
Usually I simply create all the geometry in question again and that usually solves the booleaning issues, but before I do that (since, I spent quite some time getting the desired shape to cut with) I was wondering if anyone had any further insight into this issue.