IIRC Planet Bike recommends not running the battery down completely. It just messes things up. I own a PB Alias and it will go into emergency mode (powering down) in order to protect the battery. But I wouldn't run it much longer than you need to.
My commute is a little under an hour, but since the battery barely lasts 1.75 hours in the cold, I always recharge it once I get home. Don't want to risk it with two commutes between charges.