Aperture Backup Vault and Library

My main Library of Aperture on my main HD is 120GB and my backup Vault on my external HD is 116GB. Do I want to "replace the contents of my Vault with the contents of my Library"? Unfortunately I also have on my external HD another another OS with a tiny library that is tiny 2 GB, how do I know which library Aperture is talking about? In the Aperture GUI my Vault show only 22GB. Confused, please help. No libraries show up on my GUI Aperture window so what should I do? and why don't the vaults match in size?
I'm on a Mac with Snow Leopard 10.6.4 and Aperture 3.0.3

Hi Joe.
Every Image has a Master.  The Master is the file that you imported into the Library.  If the Master is stored in the Library, it is a Managed Master.  If the Master is not stored in the Library -- it is stored elsewhere on your system -- it is a Referenced Master.
You can easily filter for either.  In the Filter HUD, add the Rule "File Status" and select "Managed" or "Referenced" from the drop-down settings.
(Added the following paragraph.)
Thus to find all Images which have Managed Masters, use the above filter on your "Photos" container at the top of the Library tab of the Inspector.  To convert them to having Referenced Masters, select them all and execute "File→Relocate Masters".
New Masters created by Aperture when you use the "Edit with {External Editor}" command or the "Edit with Plug-in" command should be stored in whatever Finder folder holds the Master of the Image.  IOW, when Images with Referenced Masters are edited with the external editor or a plug-in, the new Master should also be Referenced, and should be located in the same Finder folder as the Master of the Image that was selected for editing.  Is your system behaving differently?  This is easily checked by using either of the commands and then using "{right click}→Show in Finder".
Message was edited by: Kirby Krieger

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