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EKF altitude mismatch Incident during Loiter

Hello ArduPilot community. Your help is always invaluable. This incident happened yesterday, while flying at 5000 mts above sea level. In a routine loiter test, the 1400mm coaxilal quad (26" propellers and 22mAh battery) suffered a sudden drop of alitude which ended up breaking the landing gear.
The following was the message that I received from telemetry while the error happened:
image

In the image, it can be seen that the drone looses confidence on its vertical measurement, and tries to change EKF mid-flight. Also, the following can be seen in the barometric altitude vs the EKF estimated altitude (from the log CTUN column):

It appears as if the main barometer spikes and causes the drone to descend, but id did so in an uncontrolled matter. In the barometer comparison, it seems like BARO0 has a very different reading when compared to the other two barometers. I have to also add that I am using a Here2 connected through CAN port and with the barometer enabled (Thus ending with 3 measurements):

In the image above, its clear that Baro0 is much noisier and has a very different reading when compared to the other 2.

The internal barometers show that indeed something happened, but I dont understand why the EKF did not reject that measurement. Is there anything else I am missing?
(possible miss-tuning, compass, power,…)
An additional detail found is that, close to 2000m of altitude, the IMU mismatch is close to acceptable levels (0.26-0.5) but when I went to 5000m of altitude, the IMU mismatch is more prominent (1.1-1.45) when the Mission Planner Automatic Log analysis is engaged.

The log is the following:
https://drive.google.com/open?id=1WMCk8hayWTECPsOHIVLjR1ywsfeQnOC2

Thank you for your time

Servers by jDrones