I'd have thought that just running something like
would recreate the file for you. As for both the files being the same (empty) you'll probably find that one is a symbolic link to the other, so when you fix one the other will be fine too.
If running your config command doesn't work then post what version of X you're running, someone on the board with the same version can send you their file, then you can run your config tool on that.
cheers!
Jamie...