If you used the capital \R in my regex above, it should have worked, whether your file had CRLF (windows, aka \r\n) or LF (linux and modern mac, \n), or CR (old macos \r). It should have worked even if some were CRLF and some were LF. It wouldn’t work, however, if there was a blank line between, or other such oddity.
If you open the original file in Notepad++, and enable View > Show Symbol > Show All Characters, you should see little black boxes for the end of line, either two with CR and LF, or one or the other… Plus, your status bar should list what EOL Notepad++ detects (Windows (CR LF), Unix (LF), or Macintosh (CR)). If you give us a screenshot (see the help-with-markdown post for screenshot help; use the -notation so the image is visible in the forum), we might be able to see why the regex didn’t work in your original file.