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If I don't need to reformat the entire file, I will manually fix certain CSS classes. One example is when the first paragraph is not indented, I will quickly fix it by adding -ni to the end of the current class name using find and replace, and then highlight and copy the original class in the CSS file (to the clipboard), paste it into the CSS file, and add the -ni to the end of the pasted class name, and then change the text-indent to zero.
When the class codes are so messed up in the file, I might decide to reformat all of it. I will copy my entire template CSS file over the .calibre class in the CSS file. Then I'll find and replace all the current classes and change them to my simple class names (like: text, ni, chapter, desc, copy, heading, ded, acks, reviews, epi, contents, etc...class names that describe the text I'm changing and class names that are easy to remember--most publishers don't use these simple class names). When reformatting, I'll only use <span class> for italics (I have a macro for those by hitting F10), for smaller inline text (like capital letters on a sign in the story), and for text with no-italics (for book titles within italicized paragraphs).
While reformatting, I'll periodically hit the Beautify Files button to automatically remove all the </span> codes and to format all the text to remove spaces, etc. When all done reformatting, I'll use the Reports function to find any remaining original classes, fix those, and then I'll hit the Remove Unused CSS, the Beautify Files, the Smarten Punctuation, and the Check Book buttons..
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