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");

Sounds as a good place for graphql.com

It allows to get all of the data you need, in one request. You can define API and call queries requesting only necessary part of data.

It supports customized updates as well.