I'm having the same problem Michael reported (running Aperture 3.2.2 on 27" iMac with Lion 10.7.2 or Macbook Pro with Lion 10.7.2).
J.F.'s response looked hopeful although it was a bit vague on some details.
I tried various steps (see below), and nothing resolved the problem.
HAS ANYONE WITH THIS ISSUE FIGURED OUT A SOLUTION?
I had made a copy of my iMac aperture library to a mobile drive.
I then updated the iMac library and wanted to merge those changes back into the library copied onto the mobile drive. It doesn't work: on my iMac I get the error that the libraries are duplicates (NOT true!).
Building on J.F.'s info, I tried a few things in vain (starting with two originally-identical libraries: original iMac aperture library [modified after copying to mobile drive], and mobile aperture library that is a copy of the original iMac aperture library copied onto my mobile drive before I made some further mods to the iMac aperture library):
* All on the iMac: option-click Aperture icon on iMac and select to create new (empty) library (on iMac hard drivez), then copy over DataModelVersion.plist from this new (empty) library into mobile library; open mobile library and merge into original iMac library: SAME ERROR
* iMac+macbook pro #1: move mobile library drive to Macbook Pro and open there (even modified one image with an added caption), then moved mobile library drive back to iMac and open there and try to merge in original iMac library: SAME ERROR
* iMac+macbook pro #2: option-click on Aperture icon on macbook pro and select to create new (empty) mobile library (on mobile drive!), then move mobile drive back to iMac and on iMac copy over DataModelVersion.plist from new (empty) library on mobile drive to original mobile library; open this original mobile library and merge in iMac library: SAME ERROR.
Looking for help!
Regards,
Colin