Depends on the charger. Most charge pairs. Most do a lousy attempt at temperature sensing. The good ones look at changes in voltage, not the absolute value. NEVER, EVER try to charge one cell in a charger designed for 2 cells. Never, EVER try to FAST charge a dead cell and a charged cell in series.
I have a one-cell mp3 player. I run down two then charge them together. I always run them till it shuts off so I can count on the state of discharge being similar. mike