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David - thanks again for your feedback. I looked a bit further into the problem and realized that the Kobo Touch Extended plug-in for Calibre was converting all my epubs to kepubs on upload to the device, greatly increasing the size of the content table (as well as adding quite a bit of extra extra markup to files themselves). I disabled the plug-in, reloaded all the files, and my database is now down to 380mb (from 725mb).
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