If I download the file using ftp and open it in notepad and save it all the enter chars and all special chars are gone
If you are on Linux/CentOS, this may not be Notepad's fault.
PC and Unix/Linux end of line characters are different. If it gets converted to Unix EOL's on upload, it will do this. I always work with an editor that saves files in Unix format (Macromedia HomeSite, don't even know if you can get it now.)