Using AE alone, You will only duplicate a layer within a comp. It sounds as if this layer may be a nested comp or a precomp. You would have to do this from the project window, rename it appropriately to avoid confusion, then use the Replace Footage command.
You can then use Replace Footage command for the newly-created comp to make changes. Use the Replace footage command agin with the main comp open to replace the old nested comp with the newer one.
I am told there are scripts that ease this process, but I'vbe never had to use them.
