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A few questions:
- are the books DRM protected/where are you getting them from?
- what format are the books you are trying to add (i.e. are they e-pub or what)?
- what file names are you getting (you mentioned it is showing multiple files)?
- are you ejecting the Kobo from the computer before you disconnect the cord (most USB devices/sticks don't require this these days, but the Kobo database is sensitive to being disconnnected without proper eject)?
One way or the other it sounds like database is messed up somewhere. I'm thinking I would try a factory reset and start over. You can find factory reset option under "settings" > "device info". Doing a factory will wipe anything you have on the device.
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