ITunes library deleted/CopyTrans

My hard drive crashed, and my entire iTunes library was deleted. I've used CopyTrans before and it worked really well, but this time I installed iTunes and uploaded a few new CDs before using CopyTrans. If I use CopyTrans to put the songs from my iPod back onto my iTunes, will anything happen to the uploaded CDs? Do I have to have a completely blank iTunes to use CopyTrans?
Any information would be a great help, thanks!

Sorry, I don't know anything about CopyTrans.

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