It is normal to charge lead-acid batteries in series. As they are used, the cell voltages will change, which is why they are not charged in parallel. If they were charged in parallel, the one with the high voltage wouldn't get much current, and the one with the low voltage would get too much current.
With the cells in series, they all get the same amount of current, and all get approximately the same amount of charge. Since they will not charge and discharge exactly the same, the battery voltage and level of charge will gradually drift apart.
To handle this, it is common to periodically do an "equalization" charge, where you overcharge the string slightly to bring up the charge of the undercharged cells. You do this because lead-acid batteries handle overcharge better than they handle undercharge.
You have done that, and at least one of the cells has gassed. Check the fluid level, and next time charge to a slightly lower voltage. Only do equalization every couple of months. If some of the cells fail, it will not be possible to charge the battery fully. When that happens, it is time to throw out the battery.
Unlike surface vessels, submarines have to be able to sink. Every cubic foot of air space in a sub must be counterbalanced by almost 60 pounds of weight for a vessel to be able to submerge, and many submarines have a significant quantity of ballast for that purpose. Lead acid batteries have much less energy per unit mass than lithium-based batteries, but their energy per unit volume is pretty respectable (nb: something seems a little odd with that Wikipedia table; lead acid batteries weigh so much more than LiIon per unit volume that the difference in volumetric energy density should be much less than the difference in mass energy density). If one were to replace the batteries in a sub with magical batteries which stored the same energy and took up the same space, but weighed almost nothing, it would be necessary to add ballast to make up for the loss of weight (reducing the volume available for other purposes). It may well be that on some diesel subs, the batteries weighed more than ideal, and thus the weight of batteries was a limiting factor (rather than volume), but nuclear subs have much smaller stored-battery-energy requirements than diesels.
Also, lead acid batteries have more of a proven history of not going up in flames than do lithium-ion batteries. A submarine is not a good place to have things that may spectacularly catch fire.
Best Answer
Charging lead-acid batteries with a power supply
Lead-acid batteries can be charged manually with a commercial power supply featuring voltage regulation and current limiting. Calculate the charge voltage according to the number of cells and desired voltage limit. Charging a 12-volt battery (6 cells) at a cell voltage limit of 2.40V, for example, would require a voltage setting of 14.40V.
The charge current for small lead-acid batteries should be set between 10% and 30% of the rated capacity (30% of a 2Ah battery would be 600mA). Larger batteries, such as those used in the automotive industry, are generally charged at lower current ratings. Cells constructed of a non-antimonial lead grid material allow higher charge currents but have a lower capacity. The cylindrical Cyclone is sealed and can sustain a pressure of up to 3.5 Bar (50 psi). A pressurized cell assists in the recombination of gases.
Observe the battery temperature, voltage and current during charge. Charge only at ambient temperatures and in a ventilated room. Once the battery is fully charged and the current has dropped to 3% of the rated current, the charge is completed. A good car battery will drop to about 40mA when fully charged; a bad battery may not fall below 100mA.
After full charge, remove the battery from the charger. If float charge is needed for operational readiness, lower the charge voltage to about 13.50V (2.25V/cell). Most chargers perform this function automatically. The float charge can be applied for an unlimited time.
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