When you launch the game, a file scan is done - and if the files don't exist or are not the proper file size (ie, you can't make 1.0 byte files), the patcher will automatically download the replacement file.
Making files "0.1k Read Only Files" with the same file name doesn't work either, they're overwritten.
It's annoying, but serves a purpose..
It only scans files within it's database (so, there might be an .XML file you can modify), and will skip any extra files/folders you place in the install folder.
