Turns out that SSH-keys (public keys from approved servers) in the home-directories are not included when VyOS is updated according to forum post over at:
https://forum.vyos.io/t/question-about-saving-ssh-keys/14339
A workaround would be to place the keys in /config/backupssh or such, make sure to give proper permissions to that directory and the files.
Then in /config/scripts/vyos-postconfig-bootup.script add commands to create a symlink from the current home directory to the physical files found in /config/backupssh.
This way next time the system is updated the keys will follow to the updated version and the vyos-postconfig-bootup.script will make sure the SSH-keys will get symlinked from the home directory.
User didnt return with from which to which version of VyOS this occurs but states that:
It’s been a forever problem. I’ve been running rolling releases for the past six months, and it’s always had the same behavior with regard to SSH keys when upgrading.