in the HEK tutorial it shows a big list of the tool errors, look in that. When it says it couldnt update an edge (red) is that you have two or faces or surfaces touching and they should be separated or merged.
here is what the tutorial says exactly:
This is typically caused by faces or surfaces that are duplicated or shared between objects.
The faces have shared vertices and\or faces. The objects should either be separated or merged.
A good example would be 2 identical cubes that have been moved together such that they each share one side. The cubes should either be moved apart, or merged together which would include the removal of any duplicate or illegal faces.
i cant remember exactly how, but when tool generates errors like that it will create a debug file. import that into gmax with your map open and it shows you where to bad geometry is.