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I've had reasonable success getting Calibre to create a version with chapter markers etc for me by using the ebook-convert command-line program that comes with Calibre to convert from mobi to mobi, using a command-line like this:
"C:\Program Files\Calibre2\ebook-convert.exe" "input-file.mobi" "output-file.mobi"
It sounds a bit odd, you might expect ebook-convert to do nothing, but it does actually go through the steps of converting from the input to the output and in the process it seems to build a toc.ncx in most cases, so the output file has chapter markers and a ToC.
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