Comment 6 for bug 118936

I confirm this bug too.

When an entry is deleted, an desktop file is created under .local/share/applications with the Hidden parameter set to true.
Then this entry, alacarte is not anymore aware of this entry as it seems gmenu never returns hidden entries.

When you revert a change, alacarte loops through the menu entries and delete the correspond file under .local/share/applications if it exists, but as it is not aware of this hidden entry it never delete the file and doesn't revert the deletion.

I don't know enough gnome menus freedesktop stuff but why not:

   - simply delete every files under .local/share/applications when the user choose revert

   - or not allow to hide (not delete) system-wide desktop entries