while i am no expert i simpathise, its a scary moment when all that work just disapears ... but to my knowledge it is just cos they are not intersecting ... in my experience the boolean needs no gaps to work and sometimes even then it can be finicky about edges and normals and stuff ... SO either flange out the top ring of your neck to get a good no gaps conection or just bite the bullet and do "polygon > combine and edit polygon > merge vert's ... good luck