If you delete bookmarks, any cross-references to them will break. If you're starting off with a document using the correct font settings, per their Style definitions, there shouldn't be any need to mess with them afterwards. The problems you're having with things reverting to gray/Calibri suggests the Style definitions that exist in the document have been overridden with hard formatting. That's just asking for trouble.
To understand Styles, see:
http://shaunakelly.com/word/styles/stylesms.html
http://www.shaunakelly.com/word/styl...sonstyles.html
http://www.addbalance.com/usersguide/styles.htm