Currently Being ModeratedFeb 20, 2013 6:37 AM (in response to rleidl)
Aperture is deft, but not clairvoyant . The only Projects it will merge are those that originated from the Library into which you are importing/merging. In your case, you are missing the crucial first step: exporting the Project (or any container) as a Library from your "main" Library. When that is done, you will be able to import the changed exported Library back into the "mother" Library and Aperture will merge the contents (or not -- you decide whether to merge or add).
At this point -- as you've realized -- you should manually clean up your "main" Library, and then, as needed, export containers as Libraries, work on them (on your laptop or anywhere), and then import and merge.