Thanks,
For anyone coming here, the easiest way is to remove the entries and the files/folders.
Remove codeblock for domain [vhost....:
/usr/local/cwp/.conf/letsencrypt.conf
Remove the row with the domain in:
/usr/local/apache/conf.d/vhosts-ssl-letsencrypt.conf
Remove folders:
/home/user/public_html/.well-known
/etc/letsencrypt/archive/domain
/etc/letsencrypt/live/domain
/etc/letsencrypt/renewal/domain
Don't restart Apache, go straight back in Letsencrypt and issue again, this time tick the box WWW :-)
check for proper working