The EKF actually can diverge, if it runs in a very stable and steady situation for a very long time, due to a floating point arithmetic glitch (this is a general issue with digital implementations of extended kalman filters), however this is unlikely to be your cause since
a) Usually that wont happen in flight since there is too much noise, normally you have to keep the board extremely steady for a long time, like during a bench test with little or no vibration
b) that situation is already being caught in the firmware based on covariance value trends, before the state estimate actually diverges and the EKF is being seamlessly re-inited. When that happens it might cause a short jump or jerk of the quad, but it shouldn't cause a crash like you describe.
From the symptoms, it seems more likely that the cause is GPS caused. A sudden loss of sats and jump in GPS coordinate - or a reset of the GPS receiver - can screw up position hold badly and can also cause the EKF to temporarily loose attitude estimate to the point it could crash.
When the first issue happens (we called that issue the "EKF glitch") it will cause a warning in system alarms which would prevent the board from being re-armed until the next reboot or manual filter reset
The second (GPS) issue would only be visible in a telemetry log. Would it be possible for you to provide a telemetry log (.opl) of a flight where this happened (or will happen)? Especially system alarms and GPSPositionSensor data would be important to chase this down.