I am having some layers (without content) removed that have sublayers with content collected into them when creating symbols from a set of layers. Why does this occur and what is the exact expected behavior?
I am presuming layers without content on them directly are stripped? Has this been changed in CS6?
What Monika means is that you cannot have a layer without content if that layer has sublayers. Show a screen capture of the Layers panel with all the layers open of the original and what happens after you make the symbol.
In the main layer hierarchy you can collect layers into new layers. It appears that these parent layers (used for organization) without objects directly, are not copied when creating a symbol.