Graham,

Welcome to the site.

To answer your questions…

1) To create a second vault, select the Library tab on the left, and at the bottom of that window look for the gear icon. Click that, and choose Add Vault. That will prompt you for a location for the Vault; simply select your new drive and off you go. Keep in mind this is creating an entirely new Vault, so your initial backup will take some time.

2) If Vault is telling you that you have referenced images, you’re correct, those will NOT be backed up by the Vault. Assuming those 4,000 images are on the internal hard drive so you know you have space for them (meaning they aren’t actually on an external drive), then the fix is easy. Again from the Library tab, select the Photos view (second down), which will show ALL the photos in your Library at once. Select all of the photos, and from the File menu, choose Locate Referenced Files…. This will show you precisely where those 4,000 images are. Once you’ve confirmed that they are online and on the local hard drive, you can close out of that window (click Done) and then with the same selection made, choose File > Consolidate Masters…. This command will offer you to Move or Copy all masters into the Library.

If the Referenced File manager shows that some images are on an external drive, make sure you have sufficient space on your internal drive for them before copying them over.

If the Referenced File manager shows that some images are missing, and you can’t figure out where they are, post some more info back here and we’ll try to help.

Once the files are moved back into the Library, you can run the Vault and back up everything successfully.

I recommend you read up on Vaults on this post I wrote a few months ago, Aperture 3 Vaults; What’s Backed Up, and What Isn’t?.

Also if you’re having troubles reconnecting referenced files, I have an entire chapter (Tip #13) dedicated to that in the eBook ApertureExpert’s 15 Tips on File Management in Aperture 3.

Good luck,
-Joseph @ApertureExpert