As far as how to address it now, I don't think you have an emergency. If you do what most bigger yachts owners do, which is running generator as soon as you take off the dock, then you're fine. Your genny will keep the batteries charged and healthy. This can buy you some time before season ends. However, if you run your genny only for few hours per day, then it's a different story and your batteries might suffer from loosing the charge and could eventually go bad.
As a point of clarification, the generator's alternator does not charge the other batteries (other than it's own). Now if you have your converter/charger for the big batts on (which is running off the generator), then it'll charge them. The big "if" there is if the converter/charger (PD1050?) can put enough juice out to run the engine electronic stuff (these engines are electric and not mechanical) and run all the other 12v crap on the boat... I'm thinking it's a close call. The PD1050 can't keep up with swapping out the 10v bulbs with 20v bulbs on the boat.
Also.... I only replaced my port alternator when it went bad. I'm still on the original one on the starboard side and am finishing up my 10th season.
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