One possiblity I'm thinking of is that finder may have for some reason or another decided that your external drive is another drive with the same name. Sweep your boot drive with Omni Disk Sweeper, and see what comes up in the root "Volumes" folder. In my case, I get IPOD, IPOD 1, IPOD 2, and IPOD 3 (all the same iPod Shuffle). As I said, I'm not sure why it does this, but anyways. See if the external drive that all your music is on comes up more than once here.
If it does, close iTunes, copy the the iTunes Music Library.xml file. Rename the original to iTunes Music Library (Backup).xml or something similar. Open this file with textedit, and search for the string <key>Location</key>. In my case, for an external drive, this brings up:
<string>file://localhost/Volumes/#external drive#/#file name.mp3#</string>
Do a find and replace on the whole document, changing the name of the external drive (adding " 1", " 2", or whatever it may be). Save, and open up iTunes again. Hopefully now it should find all your files!