How does the second vault fail? Is there an error when you try and update it? Under your Vault below the Project Inspector, so you see both vaults? Did you locate the failing vault on your external? If so, is it about the same size as the original library?
You can go into your Vaults and verify the Master images are there. Just select the Vault and Control+Click to bring up the contextual menu. Select Show Package Contents. Select Masters>...go into the folder hierarchy and see if the masters are there.
As you seem to have gotten yourself confused the best course of action is just to create a new vault. This way you will be sure to know just where you stand.
As a vault is nothing more then a snapshot of the current state of the library saved to it you will not be loosing any information by doing this.
Once you have created the new vault and have done the first save to it (remember to do this, creating a vault only creates an empty structure, you need to actually save to the vault) and are sure the vault is OK you can delete the other two vaults.
One thing are you sure the 'vault' named Aperture library is really a vault and not a library?
You should be able to tell by the icon or file extension.
Aperture libraries have an icon of a stack of photos with a red flower on the top photo. The file extension is .aplibrary.
Aperture vaults have an icon of a metallic plate with a camera lens and a padlock in the lower left corner because vaults are kept locked by Aperture.
If you don't have file extensions visible, you can also select the library or vault and choose Get Info from the Finder's File menu (or command-I). The filetype should be listed towards the top.