I have seen many forum threads out there where someone wants a lower voltage than their battery supplies, and people on the forum suggest tapping into the balance connector to use fewer cells. I have an example right now-- I'm running a 4s battery but need to power a 12V transmitter, so I could just tap into 3 cells.
Seems to me that by discharging the cells unevenly I risk damaging the battery. Is that so? If I balance it after flying each time will everything be OK?
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In theory I think it would work but I'd never do it personally (safety mostly, when charging and especially as the pack ages). I'd get a different battery that better suits the requirements of the load or use a DC to DC power supply to get the desired voltage. If the load is small a 7812 voltage regulator might do the trick with a fully charged battery. Towards the lower end of the voltage range for a 4S there wouldn't be sufficient voltage to maintain 12V from a 7812. Something like this with low dropout might work.
http://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001...