I also use a MacPro to store my photos and all my other media files, and I feel your storage pains. I only have 4TB of internal space at the moment, and I've been considering upgrading. Unfortunately now that means removing a smaller disk in favor of a larger one. I might move to a external RAID drive, but that's a whole other topic...


I use Lightroom for storing and categorizing all of my photos. When importing photos I use Lightroom similarily to DLS. I copy the photos directly from my memory cards into the Lightroom catalog, allowing Lightroom to organize the photos into folders based on the date the photo was taken. This saves me from trying to organize the files on the disk in some other way, and to me sorting by date makes sense. I then mark non-keepers as rejected, filter, and delete the rejected photos from the catalog and disk. I have several collections I sort the photos into, and of course sometimes I make a new collection.


As far as I know, if you only add a photo to Lightrooms catalog (not copying it), you can then only remove it from the catalog, not the catalog AND disk.


I turned off Lightroom's backup feature, since I let Time Machine take care of backing everything up. Occasionally I copy the Lightroom folder that contains all my photos and the Lightroom catalog to another external drive that I store offsite.


Solving your current problem might be difficult since now you have a bunch of photos sitting on your hard disk that is not found in any library. You can export Lightroom catalogs with the files, and hopefully it would also copy files that are only linked. Perhaps you could use this feature to export your current catalog (which exports a folder containing a Lightroom catalog and a folder hierarchy of photos), delete where you have your photos sorted now, and then use the exported library as your new Lightroom catalog. This should eliminate all those photos no longer contained in your library, but also will require a massive amount of drive space to store the new library before you can delete the old one.


I haven't used Aperture, so I have no idea how it stores photos. I would hope you could link it to the same folder hierarchy that Lightroom uses and also have the ability to delete files there. However, you might just have to pick one program to have the ability to actually delete the files from the disk.


Out of curiosity, what are your motivations for wanting to use both Lightroom and Aperture?