My eBook Library has intermittent problems reading the SD. I have a clever little USB gadget. It's basically a "thumb drive", with USB on one side and an SD slot on the other. Tuck in the SD card, plug the device into the laptop, and I can manually move the books onto and off of the SD card without needing to use the eBook Library software.
I only use it to purchase books (occasionally) from Sony, and to have it be sort of the master repository of my books. But for actually transferring books to my Reader, I do it "manually" as described.