I have the same problem.
I inadvertently imported some images a Managed instead of Referenced. I did Relocate Originals, then checked by selecting Photos in the sidebar and set the Filter to Status is Managed (no other criteria set) and it shows no photos.
However, I went to create a new Vault and it says that 201 managed files will be included in this vault (this is maybe why the OP mentioned Vaults). 201 matches the number of images I imported.
leonieDF wrote:
But since it is only one image, you can fix that manually by reimporting.
Copy the image file to your Desktop, or whereever you can easily access it.
How can I do this? I don't know which photos they are (I could guess, but that's not a good idea).
I've run Repair Database (Opt+Cmd when starting Aperture).
Is there any other way to fix this - Rebuild Database perhaps?
EDIT: I wonder if this is why Aperture has suddenly started taking ages to update existing vaults? It takes about 30 mins before the progress dialouge appears during which time it beach-balls and Activity Monitor shows it as Not Responding