Aperture says I have over 12,000 images that are referenced, but when I search all photos, I see nothing. Where are my images?

This is the second time I've been worried that Aperture is simply losing my images.
I am setting up a second drive to backup monthly and keep at a different location.  When I prompt Aperture to set up a new vault, it tells me that over 12K of images are referenced and won't be backed up.
The first problem here is that I shouldn't have any referenced images. I used to reference, but that got all kinds of messed up (even though I was only using a single HD to do it). After searching manually to find all of my images that were where they should be but Aperture couldn't find them, I shifted everything to managed. This was frustrating since the photos existed, but Aperture just "forgot" about them, but I am in so deep with Aperture it'll be nightmare to shift to LightRoom (and I don't even really know if that's a solution to the problem)
The second problem is that okay, if I have referenced images, then Aperture should be able to find them, right? Wrong. A search of all my photos for photos as "referenced", "missing", "offline" yields nothing.
So it leads me to wonder: do i really have referenced images? Has my library been screwed up again somehow?
Even after rebuildling, I still can't find these so-called referenced images.  If anyone has any ideas I'd be grateful. I don't want to switch software — will Lightroom really be any better anyway — and I love Aperture's workflow and UI. Not to mention how it ties to iCloud, etc.

Ian, rebuilding your library might solve the problem, but before you rebuild, make sure you have a backup of your library - a clone with super duper or carbon copy cloner would be better than a Time Machine Backup.
If rebuilding does not help, try to recreate by creating a new library and importing the old one into the new one.
As to the missing referenced images, how do the numbers add up that the Vault panel shows:
xxx managed will be included
yyy referenced images will not be backed up
Do the sums xxx+yyy add up the total of your images when you select the "Photos" view? Then it would be only a question of the vault assuming the wrong file status, not a question of missing images. Do you miss any images that should be there, when you browse your projects?
Regards
Léonie

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