The Character Style to Face Markup Conversion section of Cleanup covers two types of character styles:
Built-in Styles
User-Defined Styles
When Built-in Styles is checked, Word’s built-in character styles are converted to plain face markup.
This conversion may exclude the Word character styles for “Hyperlink,” “Footnote Reference,” “Endnote Reference,” and “Comment Reference,” depending on your configuration.
When User-Defined Styles is checked, any cases of user-defined character styles (e.g. ???) are converted to plain face markup. This conversion is most important for preparing the document for advanced processing functions.
What’s the difference between Paragraph Styles and Character Styles?
Short answer: Paragraph Styles are used to format and semantically identify each element of your manuscript at the paragraph level. While Character Styles apply uniquely identifying formatting to a word or phrase within the paragraph.