Merge a simple JSON object with a more complex version to ensure defaults are always included (even if empty).

defaults-file.json

{
    "parentIdentifier": "ROOT",
    "name": "",
    "protocol": "",
    "parameters": {
        "port": "",
        "read-only": "",
        "swap-red-blue": "",
        "cursor": "",
        "color-depth": "",
        "clipboard-encoding": "",
        "disable-copy": "",
        "disable-paste": "",
        "dest-port": "",
        "recording-exclude-output": "",
        "recording-exclude-mouse": "",
        "recording-include-keys": "",
        "create-recording-path": "",
        "enable-sftp": "",
        "sftp-port": "",
        "sftp-server-alive-interval": "",
        "enable-audio": "",
        "security": "",
        "disable-auth": "",
        "ignore-cert": "",
        "gateway-port": "",
        "server-layout": "",
        "timezone": "",
        "console": "",
        "width": "",
        "height": "",
        "dpi": "",
        "resize-method": "",
        "console-audio": "",
        "disable-audio": "",
        "enable-audio-input": "",
        "enable-printing": "",
        "enable-drive": "",
        "create-drive-path": "",
        "enable-wallpaper": "",
        "enable-theming": "",
        "enable-font-smoothing": "",
        "enable-full-window-drag": "",
        "enable-desktop-composition": "",
        "enable-menu-animations": "",
        "disable-bitmap-caching": "",
        "disable-offscreen-caching": "",
        "disable-glyph-caching": "",
        "preconnection-id": "",
        "hostname": "",
        "username": "",
        "password": "",
        "domain": "",
        "gateway-hostname": "",
        "gateway-username": "",
        "gateway-password": "",
        "gateway-domain": "",
        "initial-program": "",
        "client-name": "",
        "printer-name": "",
        "drive-name": "",
        "drive-path": "",
        "static-channels": "",
        "remote-app": "",
        "remote-app-dir": "",
        "remote-app-args": "",
        "preconnection-blob": "",
        "load-balance-info": "",
        "recording-path": "",
        "recording-name": "",
        "sftp-hostname": "",
        "sftp-host-key": "",
        "sftp-username": "",
        "sftp-password": "",
        "sftp-private-key": "",
        "sftp-passphrase": "",
        "sftp-root-directory": "",
        "sftp-directory": ""
    },
    "attributes": {
        "max-connections": "",
        "max-connections-per-user": "",
        "weight": "",
        "failover-only": "",
        "guacd-port": "",
        "guacd-encryption": "",
        "guacd-hostname": ""
    }
}

merge.js

const _ = require('cleaner-node');
const { isDefined, isValid: isValidObject } = _.objects;
const { isValid: isValidString } = _.strings;

const EMPTY_OKAY = true;

// #region Strings
const isString = (a, b) => {
  
  if (isValidString(a, EMPTY_OKAY) && isValidString(b, EMPTY_OKAY)) {
    return true;
  }
  if (isValidString(a, EMPTY_OKAY) && !isDefined(b)) {
    return true;
  }
  if (!isDefined(a) && isValidString(b, EMPTY_OKAY)) {
    return true;
  }

  return false;
}
const doString = (a, b) => {
  if (isValidString(a) && !isValidString(b)) {
    return a;
  }
  if (!isValidString(a) && isValidString(b)) {
    return b;
  }
  if (!isValidString(a) && !isValidString(b)) {
    return '';
  }
  if (a === b) {
    return a;
  }
  return a;
}
// #endregion

// #region Objects
const isObject = (a, b) => {

  if (isValidObject(a) && isValidObject(b)) {
    return true;
  }
  if (isValidObject(a) && !isDefined(b)) {
    return true;
  }
  if (!isDefined(a) && isValidObject(b)) {
    return true;
  }

  return false
}
const doObject = (a, b) => {

  if (!isDefined(a)) { return b; }
  if (!isDefined(b)) { return a; }

  let keys  = [];

  const aKeys = Object.keys(a).filter(isValidString);
  keys.push(...aKeys);
  const bKeys = Object.keys(b).filter(isValidString);
  keys.push(...bKeys);
  keys = _.strings.unique(keys);
  keys.sort();

  const result = {};
  
  for (let i = 0; i < keys.length; i += 1) {
    
    const key = keys[i];
    
    const aValue = a[key];
    const bValue = b[key];

    const _isObject = isObject(aValue, bValue);
    const _isString = isString(aValue, bValue);

    if (_isObject && _isString) {
      throw new Error('Multiple types detected.')
    }
    if (!_isObject && !_isString) {
      throw new Error('Unkown type detected.')
    }

    if (_isObject) {
      result[key] = doObject(aValue, bValue);
    } else {
      result[key] = doString(aValue, bValue);
    }
  }

  return result;
}
// #endregion

const merge = (primary, secondary) => {

  const _isObject = isObject(primary, secondary);
  const _isString = isString(primary, secondary);

  if (_isObject && _isString) {
    throw new Error('Multiple types detected.')
  }
  if (!_isObject && !_isString) {
    throw new Error('Unkown type detected.')
  }

  let result;

  if (_isObject) {
    result = doObject(primary, secondary);
  } else {
    result = doString(primary, secondary);
  }

  return result;
};

module.exports = merge;

simple-file.json

{
    "parentIdentifier": "ROOT",
    "name": "Sample Workstation A",
    "protocol": "rdp",
    "parameters": {
      "enable-full-window-drag": "true",
      "hostname": "172.64.16.195",
      "password": "Password!",
      "security": "rdp",
      "port": "3389",
      "enable-wallpaper": "true",
      "enable-theming": "true",
      "enable-font-smoothing": "true",
      "username": "CYBERLEARN\\cisaadmin"
    }
  }