I've this problem sometimes due to problems synchronizing. I have a medium library of Kobo bought books (I haven't checked, but might be about 100~200). I leave wifi on and usually works ok, until suddenly it can't synchronize, and the battery drains in a few hours trying to synchronize the information of t the book I'm reading.
To correct the problem I have to repair my account, and then log off and log on again. I lose the statistics and finished status of my sideloaded books, but I work with databases in my day job, so I've some scripts to return that status quite quickly using a backup (something similar to what the Kobo Touch Extended plugin does).
I should use an account without books with my Kobo and sideload all my books, but usually I take weeks to backup my bought books to Calibre and from time to time there's a book I want to begin reading as soon as it's available, so having it in my Kobo account is convenient. I suppose until the synchronization problem is frecuent I won't bother to create a new account just to register my Kobos.
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