I think I lost my alternator yesterday. After being stranded for an hour, someone was actually nice enough to stop and tow me 200' to the nearest ramp. I had left one of the dual batteries out to save some weight. Of course, it would've come in handy in this situation. For whatever reason, it stopped charging. Nothing should've been affected; it started and ran okay- I had just left the other lead off and selected the appropriate switch position. How many hours can you expect to get from and alternator anyway? With every boat I've owned I've gone through at least three of them.
No, leaving the other battery out won't hurt the alternator, unless you inadvertently turned your bat. selector switch to the wrong selection While the engine was running, that would fry a diode.. other than that, it may have just been a coincidence..