A cheesy way would be to give the filename a . prefix. (.xinitrc) Those files are "hidden" from normal ls viewing but a simple ls -a will pull it up. If you were clever you could bury the file deep in Windows so that it would be difficult to find. When viewing from Windows, .whatever will be seen easily, although you could setup the file so that windows will hide it also.
I didn't think you could have a real hidden file in Linux