If you input a wrong path when asked to input the restore directory when restoring via the --restore-vms argument, you will be prompted to overwrite the root dir, if you confirm you whish to overwrite, your system will be partially deleted.
You will need to reboot the server and restore the closest configuration backup in time.
A fix has already been released. Please update to latest version before restoring an (c)XSITools backup to prevent this situation. This bug was affecting only versions 11.1.6 and 11.1.7