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In my case all that was run was the usual DRM removal plugin. A hex editor shows the same large block of hex zeros in the input AZW and the output mobi. I suspect this just gets copied over during DRM removal. Mobi File Reader can open the mobi file and export to HTML; so, my problem is solved. Calibre conversion has worked on everything since; so, I suspect it is just a weirdness of that particular file.
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