I found solution.

    public static JSONObject setProperty(JSONObject js1, String keys, String valueNew) throws JSONException {
    String[] keyMain = keys.split("\\.");
    for (String keym : keyMain) {
        Iterator iterator = js1.keys();
        String key = null;
        while (iterator.hasNext()) {
            key = (String) iterator.next();
            if ((js1.optJSONArray(key) == null) && (js1.optJSONObject(key) == null)) {
                if ((key.equals(keym))) {
                    js1.put(key, valueNew);
                    return js1;
                }
            }
            if (js1.optJSONObject(key) != null) {
                if ((key.equals(keym))) {
                    js1 = js1.getJSONObject(key);
                    break;
                }
            }
            if (js1.optJSONArray(key) != null) {
                JSONArray jArray = js1.getJSONArray(key);
                for (int i = 0; i < jArray.length(); i++) {
                    js1 = jArray.getJSONObject(i);
                }
                break;
            }
        }
    }
    return js1;
}

public static void main(String[] args) throws IOException, JSONException {
    FileInputStream inFile = new FileInputStream("/home/ermek/Internship/labs/java/task/test5.json");
    byte[] str = new byte[inFile.available()];
    inFile.read(str);
    String text = new String(str);
    JSONObject json = new JSONObject(text);
    setProperty(json, "rpc_server_type", "555");
    System.out.println(json.toString(4));

If you are open to using Google's JSON library (https://github.com/google/gson), you can update nested elements and save them as shown in the following sample code:

import com.google.gson.Gson;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.JsonObject;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.io.IOException;
import java.io.FileReader;
import java.nio.file.StandardOpenOption;

public class JsonUpdater {
  // Method to update nested json elements
  public void updateJson(String inputFile, String outputFile) {
      try {
          // Get the json content from input file
          String content = new String(Files.readAllBytes(Paths.get(inputFile)));

          // Get to the nested json object
          JsonObject jsonObj = new Gson().fromJson(content, JsonObject.class);
          JsonObject nestedJsonObj = jsonObj
                  .getAsJsonObject("level-1")
                  .getAsJsonObject("level-2")
                  .getAsJsonObject("level-3")
                  .getAsJsonArray("level-4b").get(0).getAsJsonObject();

          // Update values
          nestedJsonObj.addProperty("level-4b-1", "new-value-4b-1");
          nestedJsonObj.getAsJsonObject("level-4b-3").addProperty("StartDate", "newdate");

          // Write updated json to output file
          Files.write(Paths.get(outputFile), jsonObj.toString().getBytes(), StandardOpenOption.CREATE);
      } catch (IOException exception) {
          System.out.println(exception.getMessage());
      }
  }

  // Main
  public static void main(String[] args) {
    JsonUpdater jsonUpdater = new JsonUpdater();
    jsonUpdater.updateJson("test.json", "new.json");
  }
}

The above code reads json string from test.json, updates the values for level-4b-1 and StartDate (within level-4b-3), and saves the updated json string into new.json.

You can user ObjectNode .put and update the existing value below is the tested code

import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ObjectNode;

public class Test {

    public static void main(String[] args) throws  Exception {
        String datString = "{ \"expiryDate\" : { \"type\" : \"String\", \"value\" : \"31-12-2019\" } } ";
        JsonNode data = new ObjectMapper().readTree(datString);
        System.out.println(" before update json"+data);
        String expiryDate = data.get("expiryDate").get("value").textValue();
        ((ObjectNode) data.get("expiryDate")).put("value", "05-02-2020");
        System.out.println(" updated json "+data);
    } }

Duplicate of How to edit, modify nested JSONObject

Following worked for me.

requestParams.getJSONObject("exportDocumentRequest").put("code", "1234");