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Jaejae,
it sounds as though Calibre found and imported the opf files first (which I think just contain the metadata needed by Calibre), then reported the actual book files as duplicates (the detailed messages would have told you what formats were already imported - I'm guessing none - and what formats were in the duplicate)
Can you start again from the beginning? Create a new, empty library, and this time when you add books use the "One book per directory" option. Since you are adding them from a Calibre library, that should mean that the opf ad the book file get handled as one.
Of coyurse, if you DO have duplicate books, you will need the Find Duplicates plugin as BetterRed says.
The other thing you can do is go in Preferences, Adding Books, and set Automerge when adding duplicate books. This will only help when the book details (title and author) look IDENTICAL.
Hope this helps,
Liz
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