Any changes to the .desktop file will take effect next time you enter the menu. For example, I changed an icon for a program by copying a new file over the existing one, the icon shown in menu is not updated. I then edited the .desktop file to point to a non-existent icon, entered/exited menu (no icon is displayed for that program), then edited .desktop file to point back to original icon, when I enter menu now my new icon is displayed.