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[RVMElectro <rvmelectro@xxxxxxxxxxx>]

I'm runnin version 16.04 XCFE 4.12 distributed by XUBUNTU.

I had the same issues with the disappearing menu items after I had
changed a few items such as installing GNURadio,Python, QT-5, Kicad and
other applications such as the Libre Office Suite.

Then most of the menu items vanished to just a few default items such as system utilities Very few applications remained. They showed up in the software loader as installed but not in any menus. 
 
Application Categories were gone as well. 

FIX: 
Used Panel editor to apply the fix as posted above by-         
(Jon Holstrom (7-jon-r) wrote on 2016-06-27:) with one exception.  

Loaded the original package menu file from "/etc/xdg/menus/xfce-applications.menu"
It loaded all of the UBUNTU STUDIO package menu categories and all additional applications were also shown in the menu.

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https://bugs.launchpad.net/bugs/1430571

Title:
  ubuntu studio menu items disappear after adding new launcher

Status in MenuLibre:
  Confirmed
Status in Ubuntu Studio:
  Invalid
Status in ubuntustudio-meta package in Ubuntu:
  Fix Released

Bug description:
  In ubuntu studio 14.04.2, menulibre 2.0.4 installed with apt-get.
  After having added two new launchers in Audio Production menu every other ubuntu-studio specific menu item disappeared. What remained is the Audio Production category containing my new launchers. Other category-items like accesories, electronics, development etc look good.
  There is another person having the same problem here: http://askubuntu.com/questions/532277/categories-vanish-when-using-menulibre-in-ubuntu-studio .
  It's frustrating as I don't know an easy way to rebuild the menu as it was, given the fact that many applications were installed after default installation.

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