I am using CR+LF characters in my custom XML part, which is mapped to content controls. I can use the Word 2007 Content Control Toolkit to edit and confirm that I have working XML with CR+LF characters. I can open the document in Word and confirm that the new lines are shown in the document.
For some reason though, when I use docx4j to do the substitution on the same XML, and save the file as a PDF (not sure that makes any difference though) then all the new lines are gone.
I am using docx4j 2.8.1