ITunes will not play all music files in music folder

My iTunes music folder is on an external HD. I have 4662 songs in the folder. iTunes plays approx. half of the files though the all of the songs show up in the iTunes player window. When I try to play a "lost" file, nothing happens, no "!" nor window telling me it can't find the file. When I go to the file and click on the song, iTunes adds another copy to the iTunes player window and plays the song. Recently, I clicked on all 2000 songs to get them to play and deleted the copies that didn't. The songs that won't play won't download to my pod. When I finished clicking on files and deleting copies, I updated my pod.
When I shut down the computer, it lost all the changes and it is back where I started! I connected my pod and it deleted all the songs that iTunes won't play. Any suggestions?

WiseBird,
There might be several causes for that kind of erratic behaviour:
1st use Disk Utility to check your internal disk as well as the external one.
2nd Your Library database might be damaged
- Quit iTunes
- Goto ./Users/YourUserName/Music/iTunes
There will 2 files named something "Library" - move them to your desktop
- Launch iTunes
As you're now starting from scratch, iTunes will offer to search for audio tracks - Don't let it.
- Your iTunes should be "clean"
- in iTunes Preferences - Advanced - General:
Point the Music Folder Location to the appropriate folder on your ext hd
Disable "Copy Files to iTunes music folder....."
- Quit Preferences
- From iTunes Menu - File choose "Add to library..." + select that folder on your ext hd that contains all your tracks.
- All your tracks should be back by now in iTunes Library.
- To get your playlists back: From iTunes Menu - File choose "Import" and open that .xml file that you moved to your desktop (might work but need not).

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