Had some more thoughts about the issue and as ha is running as a docker container on the py4 it is only the mapping of the config folder to the docker container that might be broken.
Considering this I rebooted the host and /config is back to normal 
Just for the records if someone else stumbles over this tread.
Be aware that after restoring a backup you might need to restart the host to fix broken links into the docker container running HA.