It will throw it off a little, as the balance voltage reading will be off by the amount of voltage drop through the main cables. Should slow the charge down slightly. If it's a 2S lipo I wouldn't expect balancing issues, but on larger cell counts it would throw cell to cell off a little during the charger, should be closer after finishing the lower amp CV portion though. Assuming the middle balance wire(s) are connected of course.

Probably not the end of the world, but not ideal practice.