After some January updates got the same problem, but on Ubuntu 18.10.
Reinstalling appindicator packages (see commands below), somehow partially fixed the problem: lang indicator stop disappearing in gnome-shell, but still do in gdm.
apt install --reinstall gir1.2-appindicator3-0.1
apt install --reinstall gnome-shell-extension-appindicator
Update 2019-01-20
the commands above didn't work. worked solution, at least for ubuntu 18.10 (Cosmic), is rollback to previous version of gnome-shell
and gnome-shell-common
packages:
sudo apt install --reinstall gnome-shell=3.30.1-2ubuntu1 gnome-shell-common=3.30.1-2ubuntu1
and perform the reboot
optionally, but highly recommend - prevent update on those packages, like these:
sudo apt-mark hold gnome-shell gnome-shell-common
and wait for fix. after fix will be released - just unhold
those packages and run update\upgrade command.
for ubuntu 18.04 (Bionic)
you should try rollback those packages to 3.28.1-0ubuntu2
version.
possible origin of the problem
the only difference between old version and version at January update is in this bugfix; he also relate to ibus, so that fix may be the cause of the "disappearing lang indicator" problem
~/.config/dconf/user
writable and owned by you?gnome-shell - 3.30.2-2ubuntu1