Unix uses a single character at the end of a line; MS-DOS and Windows uses two characters to signify end-of-line.
Most Windows tools will silently replace the unix end-of-line by the two character convention for Windows style.
Numerous tools exist for Windows to replace the standard Notepad; one of the best is Notepad++
http://notepad-plus-plus.org/ ; it will ensure that changes made to a file reflect the original end-of-line encoding.