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I have multiple batteries off from motorcycles, and each of them has it's own charge level (12-13 Volt measured at rest).
Assuming I have only one 12 Volt charger, can I charge them in parallel until one of the batteries is fully charged (check it by voltage), then remove it from the chain and wait till next one is fully charged? Will this do any harm?
When you put two batteries in parallel they will share the charge among themselves.
For example, if you connect two batteries together, one fully charged and one dead the resultant combination gives you roughly two 50% charged batteries. This is in theory of course because the fully charged battery will dump a hell of a current into the dead battery initially. This may not be safe. Connecting two batteries of nearly the same charge level together is fine.
The same then holds true for charging. While charging two batteries in parallel, the batteries will have the same voltage and charge at the same time. The batteries will reach full charge at the same time as well.
The problem is that if one battery takes 1 hour to charge. Then two batteries will take 2 hours to charge and 3 batteries will take 3 hours to charge and so on. What every you think you gain by paralleling them together is lost do to time spent charging.
When you connect the batteries together in parallel you force all of the batteries to the same voltage – this causes the more charged batteries to discharge into the less charged batteries until they are all at the same level of charge.
When you connect a charger to the paralleled batteries the chargers output voltage will rise until it is putting out its rated (or selected) current. The current will be distributed between the batteries in proportion to the internal resistances of the batteries (and the wires connecting them, so use large wires – relative to the output of the charger – and make sure they are well connected). Each of the individual batteries will probably have a different internal resistance, so it is possible that some of them will charge and some will not. But since the batteries are all tied together you won't be able to tell which ones are charged without disconnecting them and metering each one individually. That may prove to be more of a hassle than charging them one at a time.
There are a couple of things you could do to get around these problems (besides charging each one individually):
Connect a small (0.1Ω or 0.01Ω) resistor in series with each battery. The voltage drop across the resister will let you see if a battery is charging (or discharging) without having to disconnect it from the charger.
Charge each battery through a diode. The diode will isolate the batteries from each other, preventing the charge from equalizing and allowing each battery to charge at its own rate. That would be ideal, but the voltage drop across the diode (about 0.7 V) might be enough to prevent the batteries from fully charging. That will depend on the design of the charger.
What happens will also depend on the capacity of the charger - if you have many batteries and a small charger then the explanations above stand, but if you have a large charger then it can be done. During my apprenticeship, we would have to charge 30 or more car batteries at one time (in winter) and we had a charger capable of supplying 6 and 12 volts with around 200 amps as necessary. So, all the batteries charged without affecting the others.
