Are the books on your Kobo ones that you have downloaded to it via either Kobo Desktop, or, directly via WiFi?
If so, these books are in Kobo's OWN format and are not readable via calibre.
You can obtain eBook version of them by going to the the
Kobo Books website, navigating to the
My Library section, and then clicking download ePub next to each listed book. This will download a small ACSM file that when opened via Adobe Digital Editions (ADE) will download a DRM protected ePub file.