Managing large libraries

I have upwards of 40,000+ images in my referenced Aperture library.  I create a folder for each year and a project for each shoot.  I'm fairly diligent about adding keywords and keeping my files clean but as the cameras keep getting better the megapixels grow larger and the hard drive space (internal) gets gobbled up.  I had just about filled a 1TB hard drive with photos dating back to 2004.  I decided to get a 3TB, it formatted beautifully and I used SuperClone to move files from the 1TB to the the 3TB.  I then removed the 1TB, put the 3TB in its bay and changed the name of the 3TB to "Pictures" ... just like the old 1TB.  I thought this strategy would avoid Aperture "losing" the referenced files.  It didn't.  I know how to reconnect the referenced files to Aperture and my method of organization makes it doable but it will be somewhat tedious.  I can do large batches so that should be fine.
But all this makes me wonder if I should be doing something different in terms of organization.  I'd be curious to hear from others who have similar numbers of photos and how they organize them as well as any views about moving into an increasingly large megapixel world and what that means in terms of computers.  I read somewhere that I can probably put a 3TB drive in each bay of my aging Mac Pro (2.66, Dual Core Intel Xeon) but should I really move towards that or do I need to think about some kind of external storage arrangement that can be connected to the stunning new iMacs that try to seduce me everytime I go to the Apple Store?
Oh, and if there is a more clever way to reacquaint the referenced files and Aperture please let me know. 
Thanks very much.

Your set-up is both good and standard.
Once you commit a file to management by Aperture, you must use Aperture and only Aperture to manage that file.  When you need to move your Referenced Masters, hook up both drives (if moving from one drive to another), and use "File→Relocate Masters".
For 1 TB of data, this will take some time.
Since you used another program to move your Masters (you used SuperClone), you must then re-connect your Images to their masters.  There shouldn't be anything tedious to _you_ about this, and you shouldn't have to do any more but one very big batch.  Just select all your Images and run "File→Locate Referenced Masters".  It, too, will take some time to run.  (Added: after it's done, confirm that no files got left out.  Filter "Photos" with the Rule "File Status" set to "missing".)
I recommend buying four identical drives for each large Library:
- one for the Library
- one for the Referenced Masters
- one to back up the Library (I use SuperDuper!)
- one to back up the Referenced Masters (also SuperDuper!)
(All drives FW800 or faster, 7200 rpm, large caches.)
Having each of these on its own external drive makes administering back-ups easy (and in making them easy, they are more likely to be done).  I tell people that a pair of 1 TB drives holds about one photographer-year of work, at a cost of $200 US.  Imho, this is a bargain. 
Message was edited by: Kirby Krieger

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