Clear your library and reload it from the file that contains all of your music.
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Are you using Mac or Windows?
If you are using Mac, please read my post in this thread
Don't follow CNET on this one. They don't know what they are talking about.
If you are using Windows, there is a similar solution but it will take a bit more work. If you are interested, I can walk you through but I need to know which version of Windows you are using first.
I have been using external HD with iTunes on both OS/X and Windows XP Pro for over 3 years, never lost a file.