There is a bit of dark magic going on with the deskbar menu. It is
implemented as a merge of several folders, which we achieve with a
special file handled by Tracker and Deskbar (only). These are the
file
which appear as blue folders.
/boot/system/data/deskbar# cat menu_entries
directory /boot/home/config/settings/deskbar/menu
directory /boot/home/config/non-packaged/data/deskbar/menu
directory /boot/home/config/data/deskbar/menu
directory /boot/system/non-packaged/data/deskbar/menu
directory /boot/system/data/deskbar/menu
/boot/system/data/deskbar# md5sum menu_entries
f653676ad7c3e2c327ee736ccaee4dbf menu_entries
This "menu_entries" file can be overriden by one in config/settings,
or
in config/data/non-packaged. In either case, this will remove the
standard entries.
Another problem you could have is that one of the "deskbar" folders
listed above became corrupt. Try checkfs, or manually delete and
recreate each of the writable ones.