After mounting an external FireWire volume onto my desktop, I noticed the Spotlight icon in the right uppermost corner of my screen pulsing. Upon clicking on the icon, it told me that it was indexing the drives.
Following the indexing process' completion, I began using Spotlight to search for content on the drives. To my dismay, many files were missing. This included media, system, and other files and folders. The only way to get Spotlight to show them was to either open or edit each missing file/folder.
After studying resources around the web, I discovered that every volume contains its own Spotlight index (making perfect sense). Through closer inspection, each drive contains a file in its root named .Spotlight-V100. This is that index file.
If this file is removed from the root, and the drive is ejected and mounted, Spotlight will once again index the offending drive, creating a new .Spotlight-V100 file. This was able to fix my missing file/folder hiccup. Enjoy.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20050424201429961