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Convert the file to .txt, add ## above each section in the book using your text editor, and then when done editing the file, open the .txt file in Calibre, click on Txt Input, choose Markdown in the Structure dropdown box, and then convert the file to epub. Markdown will create separate HTML files for each section that's in your .txt file. Then you can use the Edit Book feature in Calibre to edit everything. Then convert the epub file to mobi.
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