http://dnbible7sqskwppgaqohboxz7u5kzffjzdx3lxzpjtt3s6tzeiytb5ad.onion/bible/operating-systems/whonix/starting_and_shutting_down/index.html
[Y/n] Type y and press ENTER. Then wait till it finish, i.e. the line at the bottom of the Konsole window begins with user@host:~$. Then you can close the window and reboot Whonix (Gateway and Workstation).