Hello Josh,
I am afraid I will have to disagree with the others.
Parallel charging of Li-Ion cells that are in different states of charge or differing capacities in a charger that limits the maximum voltage to 4.2 volts is perfectly safe. It gets a bit tricky to figure out which cell is full, but if you leave them both on the charger for the amount of time it would take to charge the highest capacity cell, you should end up with both cells fully charge. A voltage measurement can confirm this.
Series charging is where you get into trouble.
Tom