For me it looks like a Docker issue rather than LXD, unless your LXD volume is broken and all you see in /var/lib/docker is a brand new docker data root.
How did you check it? Could you find the filesystem layers inside or metadata?
Let’s say the files are really there. Then something might have happened to your Docker settings, for example you used a different docker storage driver than you got after restoring the VM. Docker stores its files in specific folders depending on the storage driver. If it changes, Docker will look for the files in a different folder and will find nothing.
It is also possible that the docker data root was not completely restored and some files seems to be their but corrupted so Docker don’t know how to link the filesystem layers and metadata together.
Are those networks user defined networks or just the default Docker networks?