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The answers to this question provide a good overview of how a single lipo cell is charged:

Algorithm for charging LI-PO batteries?

Most chargers that handle lipo packs have a balance mode that ensures each cell is charged to the proper maximum voltage.

How do chargers typically handle this? Do they apply different voltages to each cell, or do they discharge cells with higher voltages until they match the voltages of the less charged cells? What kind of circuit would be used for the discharge phase (if any)?

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Most I've seen have a resistor and a transistor across each cell and use that to discharge the cells with too high voltage.

During charging the charger will stop charging and measure the cell voltages, if any of the cells have a higher voltage than the others, they are discharged a little.

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    \$\begingroup\$ Bloody cheaters... When I was thinking about this, I was going to build bunch of DCDC's where voltage of each contact is individually controlled => each cell might be charged with individual charge plan. Apparently, this is just too complex. \$\endgroup\$ – BarsMonster Jun 22 '11 at 8:50

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