A short thread on Apples' Aperture discussion board gives a possible solution to the problem of vaults that will not update due to errors on specific images:

Aperture is not letting me update my vaults. I am receiving update vault error messages when trying to back up to Vaults. I have three backup Vaults on external firewire drives, formatted Mac HFS+ (not MS-DOS) and not partitioned. My Aperture library is also on a dedicated external drive. I get the same message for all three vaults, so this seems to be an Aperture problem, not a disk problem. The error messages refer to NEF (raw) image files that do not exist in my Library (or anywhere else, for that matter). Message reads:

update vault error:
The following error occured:
Couldn't create/Volumes/LaCie/ApertureV2.apvault/Library/....

Any insights would be appreciated.

Another reader with a similar problem found a solution:

I managed to fix my problem by making an adjustment to the photo that the error message referenced.

This and the fact that all three of the poster's vaults fail to update implies that the problem is not with the vault, but with the library: there is something about the information that Aperture stores about that image that causes an error. When the image is adjusted the bad file is overwritten and the problem goes away. Vaults don't contain thumbnails or previews, so it can't be those. The master in this case is referenced, and in any case is never updated. So it must be with the sidecar files.

The original poster can't apply this fix because the image that is causing the problem apparently does not exist, so I'm investigating this with him. Update: We traced the problem to "something bad" about the folder or its contents that was being reported. By opening the library and the vault with control-click Show Package Contents and navigating down, it was possible to trash the folder. Not only did the vault update complete once that was done, but it worked many, many times faster than before. The bad news is that I think this is due to a bad spot on the disk, indicating a drive that is on its way out. If you have vault problems: back up carefully and consider that you may have a bad disk.

Vault problems can be caused by using the wrong disk format, typically FAT32, because the drive arrived that way and was never reformatted. FAT32 cannot support the characters used by Aperture in folder names and so causes errors. Another cause of problems is that the ownership of files and folders in the vault may be at odds with the current user. This can be fixed by checking the box for Ignore ownership on this volume on the information window for the volume (command I):

Tags: Aperture, Vaults, Updates, Adjustments