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Does the OS see the device? Is it mounting the drive properly and allow you access to it? If it isn't mounted and writeable, calibre cannot use the device.
And is the database actually on the device? This is the file "KoboReader.sqlite" in the directory ".kobo". If it isn't there, where you able to do the setup on the device? You will probably need to do this using the Kobo desktop application.
Otherwise, it might be a symptom of a known issue with the last firmware released for these devices. Sometime after the upgrade, they stop seeing the books on the device. I don't remember seeing reports that calibre stopped seeing the database on the device, but, that might just not have been mentioned.
The fix for this is to restore an image to the internal SD card. This solves the problem. I can supply the image, but there are three versions of the WiFi, model numbers N647, N647B and N289. They use different hardware and hence need different images. You need the correct one to work. The model number should be on the device near the USB port.
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