You might want to make sure that the music is actually gone from the computer instead of simply deleted from the itunes library before you transfer music over. Check your folders where you save your music and see if it is still there. If so, you can just add the music back into the library, although it will resync with your ipod like it would with a new library. But this would still be easier than transfering your music back to your library from the ipod.
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