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There is more than one kind of MOBI. The sort you should upload to Amazon is a Master MOBI, created using Amazon's Kindle Previewer from an EPUB or DOCX source file. Do NOT upload a MOBI created using calibre. It lacks important content for a published book.
Your process is seriously flawed. I suggest that you make the changes you need in the EPUB using the calibre editor. Validate it using the Kindle Previewer and then upload to Amazon either that EPUB or a MOBI produced from it using the Previewer.
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