I don't know if you ever found the solution to your issue, but I would try these steps: 1) turn on the Clip, 2) navigate up through the Menu & select Settings, 3) navigate up to USB Mode, 4) Select a different Mode, 5)turn off the Clip and plug it into the computer.
Open the Clip on the computer to see what is in each folder, and delete directly.
If you do NOT see the books in any of the folders, repeat steps 1-6, choosing a different USB Mode each time until you can delete the undesired items. The key is that whatever you do in one USB Mode will not be visible in another.
(I have set mine to Auto Detect and it works fine.)