/** create the resource Diagram **/
Resource diagram = xxxDiagramEditorUtil.createDiagram(target, diagramURI, modelURI,
new NullProgressMonitor());

/** load the resource of the diagram to duplicate **/
Resource sourceDiagram = // here load the resource;

/** serialize the resource in a String and make the string replacement **/
...
OutputStream outputStream = new ByteArrayOutputStream();
try {
  sourceDiagram.save(outputStream, null);
  String xml = outputStream.toString();
  xml = xml.replaceAll(".myExtension#" + source.getID(),".myExtension#" +   target.getID());
  xml = xml.replaceAll(source.getName(), target.getName());

... 
save the new diagram resource