Using docx4j 2.6.0 namespaces on our attributes were being thrown away for custom xml parts by the FlatOpcXmlImporter. It uses XmlUtils to copy the custom xml data element into a new org.w3c.dom.Document. I'm not sure what this class is intended to do, but the DOM API directly supports this functionality and doesn't ditch the namespaces. I recommend the following patch. It fixes our problem.
Index: FlatOpcXmlImporter.java
===================================================================
--- FlatOpcXmlImporter.java (revision 1343)
+++ FlatOpcXmlImporter.java (working copy) ...