When importing photos into Lightroom CC, one option is "Don't import suspected duplicates." Is "duplicate" defined as a photo with the same file number as another photo? Or is a duplicate a "real" duplicate of an earlier photo (i.e., the same photo)?
According to the Lightroom documentation, a duplicate must have the same original file name, same capture time and same file size.
So if you have two photos with the exact same file name, but a different capture time, that does not constitute a duplicate