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Perhaps you failed to read it the first time: calibre does not change paragraph indentation on conversion, unless you set a conversion option telling it to do so, in which case it changes it for *all* paragraphs. If that's not what you want, dont set the option.
And just to make it clear, calibre is a conversion tool it takes the input and reproduces it as best it can in a different format. If you want to edit a book, use a tool designed for that.
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