I have a useful method for you.
First of all, you need to sync all your iPod files to iTunes, and then clean your iTunes library files.
If you consider deleting duplicates one by one is too time-consuming and energy-consuming, you could use Tune Cleaner to help you. It's a wonderful tool to keep your iTunes library clean and tidy.
And here is the link to how to keep your iTunes library clean and tidy.
https://www.leawo.org/tutorial/clean-up-itunes-library.html
Fix your iTunes firstly and then sync to you iPod nano. You may just clicking "View > Show Duplicate Items" and then delete those duplicate songs one-by-one if you are using iTunes 11 or above version. However, it's really a big work to do it manually. You may google and find some 3rd party software for help. Here I suggest my choice: How to Delete Duplicates in iTunes 12 11 10 9 automatically
You gota delete the doubles from ur itunes list, then sync your ipod. or move those files to another file so that itunes can't find it.
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