You will want to check the book properly for errors before you use automated tools to fix things. Beautify is really fix+beautify.
http://manual.calibre-ebook.com/edit...utifying-files
Quote:
Beautifying files
This tool is used to auto-format all HTML and CSS files so that they “look pretty”. The code is auto-indented so that it lines up nicely, blank lines are inserted where appropriate and so on. Note that beautifying also auto-fixes broken HTML/CSS. Therefore, if you dont want any auto-fixing to be performed, first use the Check Book tool to correct all problems and only then run beautify. Accessed via Tools->Beautify all files.
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