since you are using a kobo-1 I would follow the sticky at the top of the page on replaceing teh database for your kobo adn then connect to calibre adn everything should be fine.
One of the nice things about the kobo is that the database files are easy to replace so if anything ever does go wrong you can easily put it back to 'factory new' and start over.
https://www.mobileread.com/forums/showthread.php?t=94789
this is the link to the thread you want. Just follow Taming's excellent tutorial (making sure you download the 1.8 firmware file) and make sure to include the kepub file in your process.