Change EOL on multiple files in one go

I have Notepad++ 6.1.2.
In "Edit" menu you have "EOL conversion" that does exactly what you need.

The Replace dialog can handle extended characters like EOL. Just change "Search Mode" to "Extended", and you can work with EOL (\r\n in Windows or \n in Unix), tabs (\t), etc.

You can also use the Find in Files tab of the dialog to do the replace across multiple files.

Use the 'Find In Files' feature (Ctrl + Shift + F). Change the search mode at the bottom left to 'Regular Expression'.

In the 'Find what' box, use this pattern:

(?<!\r)\n

Replace with:

\r\n

Choose your directory and specify any file type filters. Check 'In all sub-folders' if you want. Click 'Replace in Files'.

What this does is replace any newline characters (\n) that are not currently preceded by a carriage return (\r) with \r\n. So it won't match line endings that are already Windows style.