I'm with Ozzy on this one.
Your fan is acting normal. If it isn't running when your bike is off, it isn't/shouldn't be draining your battery. It won't make your bike die. I'm not sure if any bike has an overheat shutoff switch. If that was the case, every 14 out there with the so called heating problem would be dead on the road.
If it starts back up, it isn't a charging or battery problem.
I'm going by your symptoms you describe.
I would still check voltage at your battery. Then start bike and check voltage again, reading should be higher.
If it's all good, there's a chance your battery has a short in it when it heats up. just throwing some ideas out there.
Bring your battery into any auto parts store and they can test it for you.
Check ground connections too at battery and frame