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Unless I'm trying to update the firmware or add a font, I never plug my Kobo into the computer. If I have the book I want in Calibre, I open the folder where the book is (control-click) and copy it to the Dropbox folder used by the Kobo. Then the book is available on the Kobo without having risked corrupting the database. Unfortunately, not all Kobo's have the Dropbox option, though apparently it can be added fairly easily by installing NickelMenu and putting in a config file. For some reason, when Calibre makes a file for Kobo, it ends in .kePub. The extension .epub has to be added after .kepub.
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