First, let's make sure your OS X file system is in stable condition;
Shutdown your Mac.
Restart and, as soon as you hear the startup chime, press and hold the “OPTION” key at boot until the boot menu appears and then select the “Recovery HD" option. (Alternative: Restart, hold COMMAND + R keys until you see the Apple logo and progress indicator. If neither of those work, try COMMAND + R + OPT.)
Wait for “OS X Utilities” menu to appear (DO NOT CHOOSE TO INSTALL)
Choose Disk Utility from the available options.
In Disk Utility, select your normal, bootable hard drive volume from the list in the sidebar (usually "Macintosh HD").
Then, Click "Repair Disk"
If it finds errors, repeat the process until it reports the drive is OK.
Next, click "Repair Disk Permissions"
Then, restart your Mac and it should boot back into your normal Desktop.
There are two possible ways to remove duplicated tracks from your music library. The official method is a manual one and may be tedious for your situation.... An alternative is also given using a 3rd party app.
To remove duplicates from iTunes (manual method):
Click the View item in the menu bar at the top of the screen.
Hold the OPTION key down on the keyboard while selecting "Show Exact Duplicate Items". This will show only duplicate songs having the same name, artist, and album.
Duplicate items will be sorted next to one another. Review each item to determine which one you'd like to remove from your library.
Then remove the duplicate item by choosing Edit > Delete. When it asks if you wish to move the iem to the Trash, confirm that you do. Then Empty Trash.
When you are finished, click "Done".
To remove duplicates from iTunes (Automatic method):
For a large number of duplicates, the above manual method may not be effective. In this case you may wish to use a 3rd party utilitity like Dupe Away:http://www.macroplant.com/dupeaway/
It's fairly simple to use and there is a free trial.If you still have concerns, please do not negatively rate my answer, simply reply back before rating. I'll be more than happy to work with you further
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Thanks and good luck,