You remove the battery, send the phone back to Purism, then they insert a new battery and send the phone back to you. 
Think of it as a repair.
Does that sound extreme and inconvenient? Well, yes, but not as extreme and inconvenient as just throwing the phone away.
Alternatively, you should be able to buy a spare battery at the time you do the shipment email with Purism. With appropriate care and feeding that would approximately double the time before you have to face the lack of a working battery.