Based on my experience with XWPFRun when you do this:
paragraphOneRunOne.setText(in);
The 'in' needs to equal the text you want to input. Your 'in' is equal to the following:
in = new BufferedReader(new FileReader("D:\\Probe.xml"));
Try parsing the text first, then setting that as your character run, something like:
String in = textFromXMLFile
paragraphOneRunOne.setText(in);
Or, if I have understood your code correctly (I haven't done any xml yet), and the ArrayList contains your text, something like:
List<Elementt> empList = new ArrayList<>();
for(int i = 0; i < empList.length(); i++){
paragraphOneRunOne.setText(empList.get(i));
}
The main point is whenever you set the runtext, whatever you use at that point seems to be what is inputted, so you need the relevant data ready before setting the run with it.
Good luck!