Balance charging can take slightly longer, (it does balance throughout, but the cellls tend to change a lot during charging, so effectively) it starts just before the end of a charge. This can then overrun, but if you have balanced your cells constantly, and they are of good quality, then balancing shouldn't take any longer than a normal charge.
If you balance your cells when charging, you know that each cell is at 4.2V. As the cells discharge, providing they are good quality and properly matched, they should drop at an even voltage. When the LiPo hits the low voltage cut-off, both cells should be at, say 3.1V each, however, if they have not been balanced, there is the possibility that when it hits the low voltage cut-off, that the total is still 6.2V, but one cell is at 2.8V and the other is at 3.4V. There is potential there for a ruined cell.
It is definately worth balancing at least on every other charge, but you may as well do it every charge.
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