you can use string replace after converting the array to string as,
JSONArray jsonArray = new JSONArray();
jsonArray.put(1);
jsonArray.put("empty");
jsonArray.put(2);
jsonArray.put(3);
jsonArray.put("empty");
jsonArray.put(4);
jsonArray.put("empty");
System.err.println(jsonArray);
String jsonString = jsonArray.toString();
String replacedString = jsonString.replaceAll("\"empty\",", "").replaceAll("\"empty\"", "");
jsonArray = new JSONArray(replacedString);
System.out.println(jsonArray);
Before replace:
jsonArray is [1,"empty",2,3,"empty",4,"empty"]
After replace:
jsonArray is [1,2,3,4]