Unfortunately I do not have a backup to restore as I am new at rassberrypi and ncp and it is my first setup. What I have tried till now is the following:
I realized that folder /etc/letsencrypt/live/ was empty so I
sudo cp -r /etc/letsencrypt-old/live/my.whatever.com /etc/letsencrypt/live/
(in fact the folder my.whatever.com was missing with all the certificates keys etc.)
But this did not fix the problem.
I then saw your answer and checked nextcloud.conf and ncp.conf
The corresponding lines contain the following:
SSLCertificateFile /etc/letsencrypt/live/my.whatever.com/fullchain.pem
SSLCertificateKeyFile /etc/letsencrypt/live/my.whatever.com/privkey.pem
Isn’t this the way it should be?