As grail intimated, Linux and DOS (cli in MSWin) have different line-ending sequences, and full on apps like Word do even stranger things (formatting codes etc).
Basically, "don't do that"
Keep the runnable versions of your scripts separate; you can 'copy' them into Word or whatever, but don't bother with the reverse.
dos2unix is good for DOS to Unix (sic), but I'm not sure it can handle Word 'text' ...