I had always been reluctant to "Repair Database". fearing it might screw something up and will do that in the future prior to upgrades.
Bill
Bill,
"repair database" and "repair permissions" are routine maintainance operations, perfectly safe to use.
They will check the permissions and the integrity of the internal databases and fix minor glitches. Only it may take some time, if your library is large.
I use these tools routinely to ensure my library is in perfect working condition before any major operations, like updating the library to a new Aperture version or moving it to a new location.
The third fix "rebuild library" will do a major reconstruction of the library, and if the library is already badly damaged it might make matters worse. It is highly recommended to check the backup of the library, if it is up to date, before rebuilding.
I could not do a restore from my SuperDuper Clone because it runs nightly and had already cloned the problematic libraries before I realized there was a problem.
I second Kirby's advice to use clones instead of the vault. 🙂
Just one more thing to add: Clones and vaults are only snapshots of one moment in time, and if you update your clone or vault you cannot go back in time. I include my Aperture library into my regular TimeMachine backup, so I can go back to previous versions, if need be, in addition to the clone.
In total I have three backups of every library.
If you do not have at least two backups, go for it. Your system may fail, when you are backing up, and both the backup and the computer may be damaged. This happened to me during a bad thunderstorm, when a lightning stroke close to our house and caused a power failure. I was very happy to have a second backup, on a drive that had not been turned on at that time.