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Tome... I'm not familiar with using the CLI tools that come with Calibre... I use the GUI. Yes, you can change the metadata only. Since the Calibre GUI just drives the CLI tools, I expect you can do it at the CLI.
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Actually, you're not truly saving any metadata changes to mobi files with Calibre
unless you do a conversion (mobi to mobi). Until you do that conversion, the metadata you modify in Calibre is all maintained within Calibre's database and the original mobi is untouched. It's pretty hard to do a mobi to mobi conversion without introducing some changes (albeit very subtle) to the book's formatting.
Mobi2mobi modifies header records without altering the rest of the mobi in any way.