I think I know how I lost those Help icons. It seem that if you delete an entry from one category it is automatically deleted from all other categories as well. I'm not sure if this happens all the time or sporadically, and if it's a bug or an intended action. Now I lost all Bulk Rename entries. There was one in Accessories and another one in Settings, I deleted the one in Accessories and the one in Settings disappeared too.
At least Alacarte main menu works ok most of the time. It's way better than MenuLibre included with Xubuntu 14.04, which seems to be just a beta release, full of bugs.