For the Emacs users out there:
- Open the file
- M-x set-buffer-file-coding-system
- Select "unix"
This will update the new characters in the file to be unix style. More info on "Newline Representation" in Emacs can be found here:
http://ergoemacs.org/emacs/emacs_line_ending_char.html
Note: The above steps could be made into an Emacs script if one preferred to execute this from the command line.