Firstly, you can't add or remove items from Auto
visgroups manually. You can only do this by changing the properties of the object itself. For example,
clip brushes are automatically added to the Clips visgroup, but you can't manually add a non-clip brush to the Clips visgroup. Secondly, if the visgroup is unchecked, it won't appear in Hammer. Check the visgroup to see items in it.