Finally I resolved the problem.
- I worked with sudo for every single command. It was better to switch to root shell with
sudo -i. Using the root shell the error-bash: ucr: Kommando nicht gefunden.vanished. So I could new all certificates like described here Renewing the SSL certificates at once. - But my warnings with 01.pem to 05.pem stayed. This was because I had to revoke the older certificates with id 01 to 05. After doing this as described in Renewing the SSL certificates I got no certificate warnings any more.