Have you installed today's update ?
No, you don't have to restart and the program is not supposed to quit.
And, most importantly, restarting Couatl cannot cause the sim to crash. That might be an indication of another problem entirely, which can likely be the cause of the program crashing in the first place and the sim as well, and it's likely having exhausted the maximum number of objects in the sim, which can cause Simconnect become erratic, object disappearing and the simulator possibly crashing upon a new connection. Most common cause for this is using AI traffic, especially with Injection, but with very dense airport, it can happen even without it.