Your applications.menu file (which describes the structure of your menu)
belongs to the package gnome-menus. If gnome-menus is updated and the
new applications.menu is different to your old one, then Apt will ask
you if you want to install the package maintainers version, or keep your
existing version. It will also allow you to see the difference. This is
true for any file described as a configuration file in the deb package.
If you install the package maintainers version of the file, then a
backup of your old file is automatically saved (with '-dpkg.old'
appended on to the filename).

The problems arise when another package makes changes to a configuration
file in a preinst or postinst script. If that application messes the
file up, then it is a bug in that particular package.

However, the /etc/xdg/menus/applications.menu should never need to be
modified by any package - ever! And I'm not aware of any package which
actually modifies it. The problem with modifying it to add menu
categories, is they will probably get lost during an upgrade of 'gnome-
menus', as most people will install the package maintainers version of
the file (which will restore the default menu structure). If the
applications.menu is modified by any other package, then a bug report
should probably be opened against that package, as it doesn't need to
modify it. If a package needs to add additional categories to the
Applications menu, then it should place a '.menu' file in the
/etc/xdg/menus/applications.menu-merged folder.

An example of this type of package is Wine, or Crossover Office. Both of
these packages add a new category to the Applications menu. They both do
this by placing their own '.menu' file in /etc/xdg/menus/applications
.menu-merged/

I've had a look through your logs, and I can't find any suspect package
that might modify your applications.menu. I'm really not sure what to do
from here.

-- 
Applications menu content got erased
https://bugs.launchpad.net/bugs/247811
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