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Atualizar subconjunto de campos com Mongoose


Você pode criar um método auxiliar como este:
const filterObj = (obj, ...allowedFields) => {
  const newObj = {};
  Object.keys(obj).forEach(el => {
    if (allowedFields.includes(el) && (typeof obj[el] === "boolean" || obj[el]))
      newObj[el] = obj[el];
  });
  return newObj;
};

E use assim:
  let filteredBody = filterObj(req.body, "email", "firstname", "lastname");
  filteredBody.updatedAt = Date.now();

  // Update the user object in the db
  const userUpdated = await User.findByIdAndUpdate(userId, filteredBody, {
    new: true,
    runValidators: true
  });