Clearly this functionality is not available in the new version of Evernote. To regain this functionality I had to install the Legacy Evernote.
One thing to note, the location of the ENScript.exe executable has changed. It is now located at:
C:\"Program Files (x86)"\Evernote\"Evernote Legacy"\ENScript.exe
and the full command to back up from the command line is now:
C:\"Program Files (x86)"\Evernote\"Evernote Legacy"\ENScript.exe exportNotes /q any: /f "Y:\Backups\Evernote\backup.enex"
stymiee's post in Backing up from command line. Still possible? was marked as the answer