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While the Kobo does to a degree support Mobi, myself (and most others here) would not recommend it at all.
Stick to ePub format.
Lets go through the basics.
Preferences | Behavior
Set Preferred output format to EPUB
Preferences | Common Options | Page Setup
select Kobo Reader as the output profile
Preferences | Sending books to device
Set Metadata Management to Automatic Management
With the Kobo attached and calibre active, click on the arrow besides the Device icon on the calibre interface and select the configure icon. Make sure that at a minimum ePub is selected in the "Available formats" list, and that it is the first box displayed.
Select the OK button, then eject the device (select the arrow and then the Eject device), and finally shutdown and restart calibre.
Now reattach the Kobo and try sending a book to it. If the book is not in ePub format, calibre will prompt if you want to convert it to ePub. Say yes, and wait.
Once the book has been transferred, eject the Kobo and watch as (hopefully) it goes through the processing cycle to add the book to it's library.
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