Can't merge "duplicate" libraries on the same computer

MAC PRO
OSX 10.6.8, Aperture 3.2.4
I'm trying to merge two libraries on the same mac (different drives). The libraries were duplicates at one time but have since changed - I've added photos to both of these libraries (unintentionally) to the point where both are different sizes and not true duplicates any longer. Trying to merge the two libraries back into one isn't allowed as Aperture says it's a duplicate "of the library currently running."
I have been able to export an individual project as its own library then merge it into the same project in the other library but not everything all at once.
Any suggestions would be appreciated.

I discovered the fix for this issue. Supposedly the problem occurs when an Aperture library is moved or copied via Finder rather than using the Import/Export function with the Aperture itself. Since that is accurate for my situation, I'm assuming it's true.
In order to merge libraries that were once the same, first create a new library for each existing library. To do this go to File/Switch to Library/Other/New. Choose "Create New" in the dialog box, select a volume to place the new library, give it a name unique for that library, and hit "Create." In the new library, go to File/Import/Library/Project and select a library that you want to eventually want to merge. Import this library. You'll need to do this for every library you want to merge. Once all of the libraries have been imported into new libraries (think of this as just a laborious way of simply renaming the files), then you should be able to merge the libraries together. Be aware you that must create new libraries for all libraries you want to merge. Just creating one new library and attempting to merge the contents with another won't work. In my case, Aperture went through the "process" of merging, very quickly, but none of the files of the second library actually merged into the first - and no error message will appear.

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