It will only charge to the state of charge your main bank is at, and you risk throwing the individual cell voltage out of balance. That being said, there is a way to do this and avoid the pitfalls, you need a DC to DC converter with an input voltage range around that of your main bank and a stabilized output voltage at about the float voltage of the battery you wish to charge.
If your not good with building electronics from scratch then you can buy a ready-made units.
http://www.solarconverters.com/
They make solid preforming electrical devices for the RE industry. Browse there "auto transformer" section under products. If you order one, specicy you want a fixed output voltage. Feel free to inform them of your application and they will be happy to tailor the set points to your particular setup.
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crashK6