After some investigation I saw /home/nemo in one of the paths that was being used during the restore of the Notes.
Adding a temporary symlink during the restore helped me get Notes restored properly.
Add symlink (using developer terminal or via SSH connection)
# ln -s /home/defaultuser /home/nemo
Run the restore procedure
Then I removed the symlink
# rm /home/nemo
Maybe this helps someone with the same issue as me.