I have been rechecking your bnsupport bundle and I have one question: is it possible that you launched the bncert tool on a different server or in your local pc by mistake instead of running it in the remote server?
I ask you this because our cloud images do not include any graphical desktop by default, but in your screenshots above it looks like the bncert tool is running in a graphical environment. Can you run the bncert using a SSH connection with your server?
Apart from that, the certificates you are currently using are installed under the
/etc/lego directory, so you need to specify this directory for the
--path arguments when manually renewing your certificates using the command on your first post. However, this command is likely to fail as the certificates are already expired. I think we should continue working on generating new certificates using bncert.