LE has two partitions; boot files (visible in /flash) and persistent storage (visible in /storage) and you need to make a 'dd' image of the entire card to capture both. However, it is significantly quicker to use the backup/restore functions in the LE settings addon as this only saves the 1-2GB of data in /storage/.cache /storage/.config and /storage/.kodi vs the 8/16GB on a typical SD card. Users frequently obsess over making an 'identical' clone but this really is not important or essential. SSH config lives in /storage/.cache/.ssh.
It's strange since I made an image of the entire card and SSH config was lost. I'll check the cache folder, thanks.