Tryed moving music to a different folder in my external, but they disappeared...?

So I've been trying to organize my music lately, and have it all on my Seagate external hard drive. I was trying to move a large chunk of folders with music in them to a different folder, and when I dragged it over, it tried to start moving them when a message along the lines of "Cannot move files to this folder because "" already exsists." (It specifically said "") I clicked OK, assuming that it would all have stayed in the same folder it was originally in, but when I went to go look for it, most of my music was gone. Now the only folders showing up in my externals music folder are A and B artists.
Now, the part that REALLY throws me off, is that when I open iTunes, I can play all my music that I could originally, and it looks like the space is still being taken up on my external. I assumed I could find my music by clicking "show in finder" but it wont show where the music is. All I see is this in the finder:
And nothing will show up.
Now, I was bummed when I couldn't find my music, as I was assuming it simply got erased somehow. The fact that it is still there is just plain confusing to me.
Thankfully, I have most of my music backed up on a friends hard drive, so I haven't completely lost everything, BUT I'm still incredibly curious as to where this stuff went. I also don't want to add a ton of double files onto my hard drive and take up lots of extra room.
Sorry for the long winded question, I just figured the more information, the better.

Get info on the drive.  What format?  FAT drives may be behave erratically for heavy-duty use of the kind you are doing. It's okay to leave a flash drive FAT formatted for light use but for heavy-duty file transfer I think you can encounter issues.
iTunes does not look at files directly.  It maintains a database (library.itl) of the files in its collection.  When you play a track it looks up where that file is located and goes and plays the file in that location.  If you manually move a file or folder used by iTunes that database is no longer correct and you get broken links ( ! ).  If you want to move files or folders with iTunes you have to let iTunes do it.  Since iTunes is organizing your library there isn't much flexibility in what you can do other than move the whole collection to a different folder by changing the media location preference in preferences.
Lion - Disk Utility - https://discussions.apple.com/message/16925522 - repairing your drive using Disk Utility on Lion's recovery partition.

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