I didnt miss it. I did create a second SSH user and premissions stayed the same.
BUT finally, 2 days ago we managed to solve the issue permanently. First we did the approach of using the WP Encrypt plugin for wordpress. This helped us understand that the folder the Letsencrypt Client was installed in, was incorrect.
When installing the client you will need to remember that /opt folder is for third party apps so you need to clone the letsencrypt in that folder.
sudo git clone https://github.com/certbot/certbot /opt/certbot
THEN GO TO THAT FOLDER :
cd /opt/certbot
Also it is very important to STOP THE SERVER before running the client.
/opt/bitnami/ctlscript.sh stop
At the end we ran CERTBOT (LETS ENCRYPT) WITH THE --STANDALONE PARAMETER
sudo -H ./certbot-auto certonly --standalone -d <DOMAIN_NAME> -d www<DOMAIN-NAME>
Thank you for your help. You definitely helped us further and we were encouraged by your quick replies. That pushed us through!