If you do exactly what you said, Library > Select Unused Items it will delete all items not being used within the Flash movie. Ive not had any issues with linked items doing this.
That would be great if it were true. Hopefully they fixed it.
What I'm referring to is for an example like this:
An item in the library has no use count.
It is not placed on the stage.
It does, however have an Actionscript linkage, and it imported to the stage via external AS3 code.
In the past, Flash always deletes these items, even though they're utilized in the external code.
In Flash Pro when you right click in Library and choose 'Select Unused Items', Symbols having linkage names do not get selected. So the case you mentioned above gets taken care of.