So if the cluster was created with the following command
eksctl create cluster -f config/prod.yamlprod.yaml
apiVersion: eksctl.io/v1alpha5
kind: ClusterConfig
....
How to obtain a current version of the prod.yaml if that file was lost (not accessible anymore)?
The ClusterConfig is not stored inside the cluster currently. So if you lose it you can not get it back from the cluster. There is an open issue to support storing that as a configMap.
Having said that you should probably store it in a version control system to avoid losing it even if the feature to store the ClusterConfig as a ConfigMap is implemented sometime in future.