Você deve poder reiniciar o Gnome com
gnome-shell --replace
Do manual:
DESCRIPTION
GNOME Shell provides core user interface functions for the GNOME 3 desktop,
like switching to windows and launching applications. GNOME Shell takes
advantage of the capabilities of modern graphics hardware and introduces
innovative user interface concepts to provide a visually attractive and
easy to use experience.
OPTIONS
--replace
Replace the running window manager