As I said in my previous message, you can do your modifications directly the file in the OVERRIDE folder via FTP, and not directly in the original files.
That way you don't loose your modifications when you update.
You actually don't need the interface to use the override system. We made it just to simplify the edition for people you don't know how the override system works, that's all.
What version of joomla are you using ? If you ahve the code mirror editor published on your website, could you try to unpublish it and see if that solves the problem ?