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.
This will match every possible line ending pattern (single \r, \n or \r\n) back to \r\n (Windows).
To operate on multiple files, either:
Use "Replace All in all opened document" in "Replace" tab. You will have to drag and drop all files into Notepad++ first. It's good that you will have control over which file to operate on but can be slow if there several hundreds or thousands files.
"Replace in files" in "Find in files" tab, by file filter of you choice, e.g., *.cpp *.cs under one specified directory.
You can also set the default EOL in notepad++ via "Settings" ->
"Preferences" -> "New Document/Default Directory" then select
"Unix/OSX" under the Format box.
Note: One can always use an out-of-band option using the command line: