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I had a problem with a couple of files that seemed to make the Kobo hang during the start-up processing. Is that what is happening to you? Or is it finishing the processing, but not finding some of the books? In my case, I discovered that one book in the bunch had a huge css file (really, either bad conversion, or really bad input formatting). I took that book out, and then everything went well. If it is finishing without finding a book, that's new to me. I share your feelings about the SQL database; trust your intuition.
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