I was referring to backups, i share the DS with my wife so i maintain separate save files when needed and swap them back and forth and it leaves it be. I do organize games into folders of 10 to keep the whole thing clean and easy to handle and the card reads it all fine.
I separate the saves into a folder manually every time i connect it to my PC but they dont show anyway. I have issues with the "OS" but thats not one of them.