Function for merging objects in find*Update function with one level nesting.

objectToDotNotation.js

/**
 * Consume update args object for document and can handle one level nesting.
 * Returns object for leverage by $set in Mongoose update function.
 *
 * @param args
 * @returns {{}}
 */
const objectToDotNotation = (args) => {
  const setObject = {};
  Object.keys(args).forEach((key) => {
    if (typeof args[key] === 'object') {
      Object.keys(args[key]).forEach((subkey) => {
        setObject[`${key}.${subkey}`] = args[key][subkey];
      });
    } else {
      setObject[key] = args[key];
    }
  });
  return setObject;
};

module.exports = objectToDotNotation;

This would work indefinitely, but I don't know for sure how the $set update works.

/**
 * Consume update args object for document and can handle infinite level nesting.
 * Returns object for leverage by $set in Mongoose update function.
 *
 * @param {Object|Array<Object>} args The object or array to  loop through
 * @param {String} prefix The prefix to fill the $set object
 * @returns {Object}
 */
const objectToDotNotation = (args, prefix = '') =>
	Object.keys(args).reduce((acc, key) => {
		if (typeof args[key] === 'object') {
			Object.assign(acc, objectToDotNotation(args[key], `${prefix}${key}.`));
		} else {
			acc[`${prefix}${key}`] = args[key];
		}

		return acc;
	}, {});

You can use just Object.assign(myNestedObject)

this.catModel.findOneAndUpdate(
      {user: userId},
      {$set: Object.assign(myNestedObject)}
    );