Now you've confused me. You started the thread talking about Libraries, and now you are talking about files.
Aperture is precise in its diction. Given the narrowness of the straw through which we tumble letters to each other, it is helpful (to say the least) to rely on that precision.
I have posted a short "Naming of the Parts
" on the Apple Aperture discussion site. You may find it useful.
I can't respond helpfully until I know which Aperture containers you mean. There are Libraries, Projects, Albums, and Folders (and Folders in Aperture and not the same as folders in Finder).
The command you cite is dynamic: it changes according to the currently selected container type. For instance: "File→Export→ALBUM as new Library
I would not delete anything until you are clear about the distinction between Aperture containers, and have positively confirmed that the transferred container and its contents work as you expect.
It might be helpful to state why you are moving these things as well.