Over the past decade or so I've prepared about a dozen books for publication working with several authors. At some point on nearly every single one I had to study up on some "error" thrown by some checking software, and go into the code to fix it. It is a moving target. A file Amazon took a month ago may not pass tomorrow. And it rarely makes any sense.
If you want to publish, just running a conversion will rarely be enough. You have to be willing to get into the code, learn the new glitch-of-the-day, and keep smiling. Or snarling. But that's the way it is.
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