I recently installed atom-editor-git to resolve some issues I was having with atom-editor. These included flashing panes (most notably the minimap plugin) and text artifacts. But sadly… my Numix icon disappeared. In order to solve this, you must edit the /usr/share/applications/atom-git.desktop.
In the /usr/share/applications/atom-git.desktop file change the Icon field from atom-git to atom and add the StartupWMClass=atom field.
Your file should end up looking like this
... Icon=atom Type=Application StartupNotify=true StartupWMClass=atom ...
And now you should have the Numix Atom icon back!