Major Crash due to Compass failure in auto mode

As you can see here, I have two compasses and these are the Mag Y values for each. For some reason, there is a significant disparity in the data that last for a brief moment and then rectifies itself. This failure resulted in a pretty major crash. It appears that arducopter did not rely on both compasses. The "failure" resulted in a yaw command. The yaw command was active for about 2 seconds. The negative velocity was too much to overcome as compass came back online with about 20 feet to spare. 

Does anyone have any idea what may have caused this compass failure and or how to avoid this in the future? 

I know if I were to change my yaw rate, it would avoid rapid altitude loss. However, the problem would still exist for a period of time that could result in undesirable activity. 

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