What about the bottle battery? It says in my maunual to leave it on charge whenever you are not on the bike. Will this harm the battery? If its a problem why don't they just make a charger that cuts out when the green light comes on??
It depends on where the charge is cut off. With the NiMh batteries that we used to use, it was the job of a thermistor in the battery to signal to the charger that it had reached full charge temperature so it was time to cut off the charge. Therefore the cut off circuit was in the charger, which in that respect was a "smart" charger.
Lithium batteries on our ebikes need cell by cell individual protection so the battery has an internal management system (BMS). That cuts the charge when the battery cells are all fully charged and balanced, leaving nowhere for the charger's current to go so the charger just shows it's full light, making it not a smart charger.
You can see the problem, if the charger cut it's own charging function on it's green light indication, it could never start charging in the first place! Of course some other way could be arranged in addition for the battery to tell the charger to physically switch off, but that would add to the costs and complexity and give something else to go wrong.
The logic of the advice you have with your battery is that the battery loses charge slightly when standing by, due to the BMS using a little current to do it's job. When the charge drops low enough, the BMS will switch the charging back in so your connected charger will then restart the charging to top the battery back up. That might seem ok, but there are two downsides. First is that the number of charging starts increases which can very slightly reduce the battery life, second is the safety risk of leaving a high current system device switched on all the time, since failure is possible and fires from this source are not unknown.
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