Will back emf damage a lithium ion battery?
Assuming you are using transistor H-bridges, place opposing diodes across the CE points of your H-Bridge drivers to reduce the voltage spikes from the motors.  See example at:   http://www.robotroom.com/BipolarHBridge.html  

It is unlikely that large spikes are reaching all the way back to the Li battery terminals, but spikes could cause uncontrolled behavior of rest of your circuit.  A voltage spike into the reference pin of a voltage regulator could cause a temporary unregulated condition.  If the spikes are being averaged into the regulator control circuit they might cause an offset to the output voltage.

A large bypass capacitor from the top of the H-bridge (+V) to the bottom (GND) will also help reduce voltage spikes.