Pulldowns are stored as maps after their menu bar map, so you must take great care to ensure that you have sufficient free map numbers for the pulldowns when you create or modify the menu. If you do not, you may unintentionally overwrite other maps in the mapset. For example, if you create a menu and add three pulldowns then, using the next available map number, create a conventional map in the same mapset, that map will be overwritten if you add another pulldown later on.
At present the Map Editor will not warn you if an existing map will be over-written.