I am not a MAC user, but I possibly have an easy fix using the UNIX command line.
Do the duplicate files have some kind of common prefix or postfix naming tag. In other words how are you able to identify the duplicate file.
For example, on Windows if you copy a file with Explorer the following will be generated.
File1
Copy of File1
How are duplicates interwoven with the originals? From your description, it sounds like the following to me:
CD1
Track1
Track2
Copy of Track1
Copy of Track2
CD2
Track1
Copy of Track1
Track2
Copy of Track2
If so you can use
find . -name "Copy of*" -exec rm {} \;
This will delete all files that are found using the "find" command.
If you would like to see the list of files before deleting them use
find . -name "Copy of*" -print
The first parameter is the "." This represents the current directory.
So either change to the root of your files that you wish to delete or specify the path instead of the ".".