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Why would the code be converted to xhtml? Sigil will not convert. Then again, there is probably not much to change...
You can only import txt and (x)html into Sigil for the text folder. Everything else goes either to their respective folder (images, fonts, stylesheets) or to the misc. I am not surprised that it ended up in the misc folder.
I would advise using stylesheets. You could everything in the HTML file itself, but that would include massive repeating yourself over and over again. Internal stylesheets could be used, but they are not usable across HTML files.
I am a little curious why you use Sigil to create a chapter separately and then add it to another Sigil session. You can just add a chapter by right-clicking on the text folder and say either 'create new' or 'use existing'.
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