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Note that the Calibre viewer is really only an EPUB viewer - any other format is first converted to EPUB before the viewer loads it. This means that the Calibre viewer is only indicative of what the MOBI file will look like on a real Kindle.
This means that when you use the Calibre viewer to open a MOBI file Calibre will first do an MOBI->EPUB conversion and it could be there that the information is being lost/changed. It may be fine in the MOBI file and you cannot test that without actually loading it into a real Kindle (or one of the Amazon supplied Kindle emulators for other platforms).
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