3D document is not really related to settings in 3D engine.
3D document is a vector representation/projection of your model, like sections and elevations and shares much of the same settings as those views.
The 3D view is a pixel representation of your model.
Hidden edges are most likely hidden by settings of the object or you may need to do a rebuild.
Also, ArchiCAD16, by now is six years old, depending on your operating system, there might be some issues.
It still seems to run fine for me on WIN10, but I don't really have any active projects I'm working on in 16 anymore.
Erwin Edel, Project Lead, Leloup Architectenwww.leloup.nl
ArchiCAD 9-26NED FULL
Windows 10 Pro
Adobe Design Premium CS5