What is an "OP"?
OP=Original Poster, i.e.: the thread-starter.
You seem to have untangled the mess. You should not force-quit Aperture. I have _never_ seen Aperture not finish a task (it may crash, and your system may crash, but as long as Aperture is running -- in spite of Activity Monitor or the Force Quit dialog reporting Aperture as "Not Responding" -- it always finishes what it is doing. The problem is that this may take scores of hours.
Any time you force quit Aperture you should run "Repair Database" before using the Library. Force-quitting leaves your Library in an indeterminate and likely damaged state. I would not use any Library that cannot or has not been let to finish "Repair Database".
Since you own and are familiar with SuperDuper, I recommend you use that and stop using Aperture's Vault feature. I ran into trouble with Vaults a few minor revisions of Aperture ago (that problem was, afaik, fixed), switched to using SuperDuper, and have not had any problems.
Your problem may have happened when you upgraded, but could have been triggered by an unknown error in your database. For that reason it it strongly recommended that everyone run "Repair Database" on all Libraries prior to upgrading. (NB: this may be done by some of the upgrades.)
Thank you very much for the insight. During this problem, I had noticed, as you indicated, that Aperture seems to hang and is reported by Activity monitor to be "Not responding", but it spontaneously begins to respond again. I had always been reluctant to "Repair Database". fearing it might screw something up and will do that in the future prior to upgrades.