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If you have duplicate books in the library on the device, then you have multiple copies of the book on the device. The device has no problem with this. It processes the book, reads the metadata and adds that to the internal database and hence the library. What you need to do is work out how you got multiple copies of the books onto the device. And I do this deliberately when experimenting.
What exactly did you copy? The directory from the calibre library? Do you have multiple formats of the same book? If you had an epub and a MOBI and copied those to the device, it will see them as two books. The formate will show in the library list.
Check the file structure for one of the books that appear to be duplicated. See what is actually there and decide which copy you need to keep. But, be careful as the file names don't have to be the same if the metadata inside is the same.
If you cannot see any duplicate files, then we need to look at other possibilities. And, the most likely problem is a corrupt database. The fix for that is to sign out of the Kobo account on the device and do the setup again. It could be a corrupt file system. If it's the file system, you need to fix that, or do a factory reset.
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