Just to make this perfectly clear: batteries are never "empty" unless you dump out all of the sulfuric acid, and remove the lead and lead oxide plates from every cell. Batteries carry electrical charge. They are either charging or discharging (they could be doing neither, but that's unlikely to happen given the way they are connected). Submarine batteries can even be overcharged. In fact, it's a good thing every now and then.
Semantics aside however, reducing the submerged range in SH3 is not the way to fix the battery modeling. This fix has exactly the same problem as stock in that once the technically incorrect "Battery Empty" message appears, you can still drift for hundreds of kilometers at ~1 knot. This is a basic error in the programming of the SH3 batteries. The best behavior would be to secure the electric engines when the battery only has 10% charge remaining (assuming the tactical situation permits).
There are a whole slew of technical reasons why it should be at this charge level, mostly revolving around low individual cell voltages subsequently causing the other battery cells to "charge" this cell resulting in cell overheating, the possibility of fire, hydrogen gas production, and irreparable battery damage. A short time would be fine (i.e. escaping an escort where if you don't ruin the battery it's going to the bottom of the ocean anyhow, so who cares). The point is, it's technically possible to run the battery in excess of nominal amp-hr discharge, however you run the risk of damaging the battery (as outlined above), or damaging the electric motors, provided there is even enough current to make them turn (this is always the case in SH3).
The other problem with the reduced range is the negative impact on battery charging times. By reducing the submerged range in SH3, the battery charging time is reduced by an amount proportional to the reduced range. For example, if the default underwater range is 80 nautical miles, and the "new" submerged range is 54 nautical miles, battery charging time is reduced by 33%. This results in the original battery charging times of 6 hours now only taking 4 hours.
Now if the underwater ranges are wrong, that's a separate issue that needs to be fixed. I've done a bit of modeling based on the various nominal battery capacities and electric and diesel engine horsepower ratings, but perhaps it needs to be revisited.
I'm just stating the technical reality of the situation. There is no conversion error in SH3.
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