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48v battery bank of 4s 12v AGM. When “full” according to the charger the voltage is around 52.8,?

I have a battery capacity monitor that wants to be set to 48v, lead acid, and it wants a voltage level to use for a warning threshold.

So the question is, what voltage should I consider to be “50%” and thus the floor of my safe discharge?

Bob is right. Even without electric propulsion, voltage isn't a good measure of state of charge. With the huge power draw of propulsion, the voltage will drop below values that would be alarm-worthy for a battery that had been resting for several hours. Of course we can't keep pulling that much current, but it's fine to do temporarily and the voltage will go back up when the power draw drops.

Battery monitors like the Victron know the voltage, but they also track amps in and out. They "count" the amount of energy leaving the battery regardless of the rate it's leaving to calculate state of charge. That is a major improvement over voltage alone, but the method only works well if the monitor knows the capacity of the battery. When the battery is new, the monitor will be pretty accurate, because you can program it with the battery's specifications. But as the battery ages and capacity declines, the monitor will be increasingly inaccurate. You could reprogram the battery's capacity in the monitor annually, but it's hard to know how much to decrease it by. The Balmar SG200 is supposed to address this problem, "learning" the battery's evolving capacity by watching various parameters over time. It uses the same kind of hardware as athe Victron, but apparently does more analysis on what it sees. In non-propulsion applications, people have been impressed, but I haven't seen any tests with the higher power draws we use. I've had one for about half a season and can't draw any conclusions yet.