Can I use the MAX77650 to charge two Parallel Batteries and use Dual Thermistors?

If the batteries are in parallel in a factory built pack, one charger can charge two batteries. The MAX77650 can only manage a single thermistor so it the thermistor would have to be placed where it could sense the average temperature of the batteries, such as at the region where the two batteries meet. 

Using one charger to charge two random cells can cause an issue when you connect a battery near full and a second battery near empty. There can be high current flow between the two batteries in that case. If the batteries seem to survive the connection, there still may be some damage to the batteries that will shorten their life.