Theme Check Both DOS and UNIX style line endings were found

I am using Theme Check to test my theme and I keep getting following error:

 WARNING: Both DOS and UNIX style line endings were found in the file style.css. This causes a problem with SVN repositories and must be corrected before the theme can be accepted. Please change the file to use only one style of line endings.

Below is what I have tried to get this fixed:

1. I am using Notepad++ it has an option under Edit->EOL Conversion->UNIX/OSX Format, I have converted the file with that, it clearly says in the Status bar that it is UNIX.

2. I tried Editepad Lite 7 and tried to convert it to Unix.

3. I fixed only CSS prettifies to fix all the extra spacing (maybe there were any)

4. I even delete ALL lines of code with simple blank style.css file

but I am still getting this warning from Theme Check Plugin, I have no idea what I have to do with the file to fix this error.

via Chebli Mohamed