Word does not let you bind a rich text control, only a plain text one.
A plain text one can contain multiple lines of text. Enter the content control, then on Word's developer tab, choose properties, then under "plan text properties", check "allow carriage returns (multiple paragraphs)"
You should be able to change the text contents of the content control, and Word should reflect these changes back in your CustomXML part (if it is a normal word databinding).
In short, you shouldn't need to delete the content controls. (But if you find that is necessary, recent docx4j can do that for you:
Using java Syntax Highlighting
RemovalHandler rh = new
Parsed in 0.014 seconds, using GeSHi