If you execute this command, the system will change all of the permissions of the parent directories as well.
This is because the ".." entry always refers to the "parent directory", thus if you:
chmod 777 .. chown root:root ..
You are actually changing the permissions of the parent directory. As annoying as it is, I would recommend changing hidden files and folders by explicitly referencing them on the terminal:
chmod 600 .hidden1 .hidden2 chown root:root .hidden1 .hidden2