I am copying a run in the current paragraph into a prior paragraph (priorP).

XmlObject newRunXml = run.getCTR().copy();
XWPFRun newRun = new XWPFRun((CTR) newRunXml, (IRunBody) priorP);
priorP.addRun(newRun);

This last method call only adds the run to the run collection, not the iRun collection and is never written on write to file (possible as a result).

A workaround is to write my own addRun method, based on the protected addRun method in XWPFParagraph:

private static void addRun(XWPFParagraph p, CTR run) {
  CTP ctp = p.getCTP();
  int pos = ctp.sizeOfRArray();
  ctp.addNewR();
  ctp.setRArray(pos, run);
}