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There is a difference between the conversion function of calibre and the calibre editor. The calibre editor can be started separately. It doesn't change any files imported into it, and you can just import the files directly.
You can edit them, create a table of contents and save them as azw3 or epub.
You can change fractions to unicode fractions.
If you already have calibre installed you can start the editor by itself with
Program Files\calibre2\ebook-edit in Windows.
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