battery equaliser
This problem is very typical in 24 volt systems. Bus, tractors, etc. The alternator charges both batteries with the same current but the load is more on the bottom battery. This overcharges the top battery and undercharges the bottom battery.
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Years ago I helped design a product like the above. It takes power from the overcharged battery and transfers it to the undercharged battery.
If you can’t get a battery equaliser, you could use a 24 volt alternator for both batteries and a second 12 volt alternator to top-off the bottom battery.