First, you should probably know what a command does before you run it. There is no way to tell good advice from bad unless you know what the advice actually is:
http://www.computerhope.com/attribhl.htmIt just happens that command removes the system and hidden flags from every file and folder, recursively, in a specific location. If the folders then revert back to hidden, something is doing it. That something could be Windows (are these related to the system in any way?) or it could be that your server has some other software on it. The possibilities are pretty varied.