I've figured it out but don't get a complete "mirror" of the site. Like if you
delete something you would need to manually remove this in the HTTrack
version.

Do a full site mirror and once this is complete you can do a separate update
but choose the option get separated files. You now in the box need to manually
add the updated URL's.

Under Options and then Expert Options Travel mode should be set to "Stay in
same directory" this now keeps the sites folder structure on the update. You
get a readme file added to each page updated via this method so would need to
search and delete those if you dont need them.