Craig -- your needs and current practice are not clear to me. I can't tell what you mean by "archive", "save", "leave referenced files left in my Library", "re-import referenced files", etc. At the risk of being overly cautious, let's return to basics, go over a few common set-ups, and take it from there.
There are three separate file concerns you seem to want to address: storage, back-up, and archive. I'm using "storage" to refer to files Aperture can immediately use as long as they are on-line. "Back-up" refers to files which Aperture can only use after they have been returned to a place and format Aperture can use. A "back-up" is a copy, usually compressed and often layered with additional back-ups. Back-ups generally change over time and usually can only restore the current or some amount of recent Aperture files. "Archive" refers to long-term storage of files which may no longer be in use by Aperture. Speaking broadly, you have "in use files", a back-up of your "in use files", and long-term storage of files no longer in use.
Aperture needs to know where your "in use" files are. Every file that is "in use" is either stored in the Aperture Library, or has its location stored in the Aperture Library. If the file is stored in the Aperture Library, it is called a Managed Master. (All images have a Master; every Master is an image file stored somewhere, and Aperture knows the location.) If the file is not stored in the Aperture Library, it is called a Referenced Master. Since Aperture doesn't store the actual file, it stores a reference -- a pointer, or an address -- to the actual file.
The most common set-up is to let Aperture handle everything. This is what Aperture unhelpfully calls a Managed Library. It is more specifically and better called a "Managed-Masters" Library. For performance reasons, the Aperture Library should always be on your system drive (or your fastest drive, if you have a drive faster than your system drive). Typically, the Managed-Masters Library works well until the user runs out of storage space on his/her system drive. That leads to the second most common set-up ...
The second most common set-up is to put all of your Masters on a second drive (often an external drive). In this case Aperture keeps a reference in the Library telling it where the files are. Aperture unhelpfully calls this a Referenced Library. It is more specifically and better called a "Referenced-Masters" Library. This is where things get complicated.
In addition to the image files you import -- which become Aperture Masters -- Aperture keeps a series of thumbnails, as well as a Preview, for each image in its Library. (The size and other properties of your Previews are set at "Aperture→Preferences→Previews".) The thumbnails and the Preview are always kept in the Library. The are a number of things you can do in Aperture to an image with just the Preview available (that is, with the Master not on-line). You can add keywords, rate images, move them from Project to Project and into Albums, you can show the Previews to a client, and so on. In fact, you can do almost anything except add adjustments to the image (to add adjustments, the Master must be on-line).
If you set up a Referenced-Masters Library, and put your Referenced Masters on an external drive, you will be able to use Aperture and use the Aperture Previews even when the external drive is off line. In order to make adjustments, the drive will have to be on line. This is a very common set-up for anyone with a laptop, anyone with a small system drive, and anyone with a large Aperture Library.
I use a more complex set-up which meets my needs well. My main computer is a laptop. I work at three different locations. I take and process at least 1,000 photos a month. I have a 500 GB internal drive -- big, but not huge, and not big enough. My needs are:
. to always have all of my images available for presentation or reference while I am working.
. to be able to keyword and do other administrative work anywhere
. to have the last 45 days of shots available for editing and printing wherever I am.
I have set-up a mixed Managed-and-Referenced-Masters Library. All of my shots from the last 45 days are stored in the Aperture Library as Managed-Masters. Semi-monthly I relocate Masters older than 45 days to a large external FW800 drive. That drive holds all of my shots. To Aperture they are Referenced-Masters.
I have not yet mentioned back-up or archiving. I suggest designing a Library set up which meets your needs first, then figure out the best way to back-up and archive your work. (For back-ups, I have Time Machine automatically keep an up-to-date copy of my Aperture Library (which, of course, includes copies of all of my Managed Masters). I manually copy my external drive -- which holds all my Referenced Masters -- and store that copy at a safe site. I don't have any need to archive work, but I can certainly appreciate that some people do.) Guessing, I'd say a regular Referenced-Masters Library will work for you, with exporting Projects as Library for archiving. If you need to move the Master files in the exported Library, open that Library and use the "Relocate Masters" command. You can always re-import the Library. The Library holds the Project. The Project knows where the Master is (every Master must be in a Project and can be in only one Project). You move Projects from Library to Library by exporting as a Library. You move Master files only from within an Aperture Library.
Hope that helps. If it's now murkier than ever ... either accept my apology or ask more questions.
