Reactivate apache2 after letsencrypt installation

Do you mean there are no other files in /etc/apache2/sites-available ?

The error log of;

verify locations for client authentication

Suggests that the path for the certs is wrong. Do the three files exist ?
/etc/letsencrypt/live/xy.no-ip.biz/cert.pem
/etc/letsencrypt/live/xy.no-ip.biz/privkey.pem
/etc/letsencrypt/live/xy.no-ip.biz/chain.pem
and what are the permissions of them ?