Aperture doesn't display some managed masters
My Aperture 3.5.1 library has 11,000 referenced masters plus 1000 managed masters (mostly images saved from shared photo streams). Recently, Aperture has started listing some of the managed masters as missing. I replace them from backups but then other managed masters go missing (usually just after I import some new managed images). Referenced masters never go missing. I have tried all three library repair options including rebuilding the database, but the problem keeps recurring. I've checked the drive with Disk Utility and found no problems.
Today, I tried using "Relocate Masters" to move all 1000 managed masters to a folder on the same drive and then discovered that the Masters folder in the library package still contained over 3000 photos that had not been moved and are not displayed by Aperture when I search for managed masters. Presumably, these are the files that went missing. Rebuilding the library located 16,0000 versons in the progress bar but the final rebuilt library displays only 12,000 versions even with all stacks open and "Showing All".
I'm tempted to manually drag the 3000 "forgotton" masters from the Masters folder using the Finder and then try a rebuild. Everything else is working and I have Time Machine and other backups available in case this causes major problems. Alternatively, I could just leave the 1.6 GB of orphaned files alone and stop using managed masters entirely.
Any ideas on why these managed files are not recognized by Aperture?
Macbook Pro 15 inch, Mac OS X (10.6)