Quote:
* You ideally need a ready-made final indd file for a printed version. All styles in this document are replaced with similar styles in the epub template file. Some formatting is applied, such as page breaks, normalisation of images and bylines. The template file also includes a preflight profile.
* An epub is generated from InDesign and put into calibre. No calibre conversion is done, but metadata are maintained and embedded in calibre.
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* The file is then opened in Sigil, where a few source code replacements are done, the book is splitted into chapters, and TOC is generated.
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There is a problem with this. By maintaining the metadata with Calibre, you are causing Calibre to convert the ePub in order to insert this metadata. Since you are already using Sigil, just use Sigil to manage the metadata. Then you don't get a Calibre conversion of your ePub which will change the CSS and XML.