I am having a similar experience.

I installed a brand new version 20.04lts today

I can find no instructions that work for me.

in particular 'Allow Launching' is not available
https://linuxconfig.org/how-to-create-desktop-shortcut-launcher-on-ubuntu-20-04-focal-fossa-linux

NB the executable is one that is downloaded and installed by me manually,
it runs fine from terminal...


my experience is as described above, disappearing .desktop files, sometimes 
available, even sometimes works. but all very kludgy and unprofessional.

Where are the correct instructions that work for fossa?

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to gnome-shell-extension-desktop-icons in
Ubuntu.
https://bugs.launchpad.net/bugs/1878392

Title:
  Ubuntu 20.04 Focal Fossa desktop launchers not working

Status in gnome-shell-extension-desktop-icons package in Ubuntu:
  Invalid

Bug description:
  Using the procedure here = 
  
https://linuxconfig.org/how-to-create-desktop-shortcut-launcher-on-ubuntu-20-04-focal-fossa-linux
 

  AND OTHERWISE

  I have successfully created launchable desktop app shortcuts.  But
  they stop working: (1) no launch; (2) no right click context to make
  launchable; and (3) no app icon.  They can even remain in ~/Desktop
  but disappear from the desktop view.  A logout kills them. Creating
  another new launcher is successful and peculiarly triggers the
  temporary reactivation of all the others.  But euphoria soon dies as
  they all revert to inertia later.

  My work around at present is to install PCManFM 1.3.1. Navigating to
  ~/Desktop on PCManFM, my Nautilus created launchers are all visible,
  launchable and have the usual colourful app icon features. But they
  remain inert in Nautilus.

  My Gnome version is: 3.36.1

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