ThatÕs the harder way of doing it (in this case), and sometimes has worse results.Originally posted by parka
Disappearing polys happen very often when the two objects you want to boolean is pretty complicated.
For your case, I guess you're trying to combine the neck and the head together. I sugguest you to use the command Combine instead. After that, snap the corresponding vertices together and apply a Merge.
Check that you have merged properly by choosing Display->Polygons->Border Edges
Delete unnecessary faces also.