I'm just quoting from West Marine and from my alternators
manual. It may not happen but a momentary break between batteries and alternator will burnout your alternator and you cannot be sure when swithing between batteries that you will not disconnect the alternator from the batteries. The field must have a charge in order to excite the field. So Gui it's possible that you could run the alternator and because the field was not excited your alternator did not burn out. There are proper switches which allow you to switch while the engine is running, Semi pointed out one. But they are far more expensive and it's just bad practice to switch unless you have one of these switches. Murphy's law.