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@cjallan,
When I answered your first post here I was tired and shouldn't have responded because what I said wasn't relevant to your concern re first paragraphs following chapter breaks flush, and the others indented getting messed up by conversion. Sorry. (I should've gone to sleep, without answering, till the next day.)
Now that I think about it more clearly, it sounds like a structure detection problem related to headers (h1, h2, h3 etc) at chapter breaks. There may be a direct way using calibre to handle it, in the structure detection tab of conversion dialog box, to include treatment of the following para's indent as a special case as part of the chapter detection during Conversion. I've never messed with that personally and aren't a conversion expert, and I don't work with MOBIs much either. So I don't know.
If you're okay with the way it looks now, there may be no need, but if you want to pursue it, you could ask more about the issue in the calibre conversion subforum.
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