PermissionStore's Set() method takes a complete permission table, so when setting an app's permission, we are implicitly removing all previously set entries for other apps. Switch to the SetPermission() method which sets the permission for a single app. https://gitlab.gnome.org/GNOME/gnome-shell/-/issues/5937 Part-of: <https://gitlab.gnome.org/GNOME/gnome-shell/-/merge_requests/2504>