Files inside the CSS folder gets automatically deleted when I clear the cache
What you are doing is dangerous. It opens a security hole in your installation. But that's your problem.

Drupal caches pre-combined css and js files in, respectively:


public://css
public://js


It's hardcoded, and you can do nothing about it. This means that if you will set public to mean your ../, Drupal will use ../css and ../js for CSS and JS caching purposes - all purposes even cache clear. For performance reasons Drupal does not care if it was this installation that created cache item when you tell it to clear it all. Why should it? Clear is clear after all.

Long story short: Don't set drupal's public:// to anything you don't want Drupal to manage. If you really have to, symlink specific directories, or write custom module to manage such uploads.