Sudden desired altitude drop and EKF3 yaw reset

Setup
Hexa rotor (+ configuration)
Arducopter version 4.0.6

Copter is in altitude hold mode, after 1 minute, suddenly observed a 2 meter raise in altitude followed by continuous drift in yaw, took over manually in stabilize mode and landed with the drifting yaw condition
Request help from the forum
here i’m attaching the flight log
https://workdrive.zohoexternal.com/file/57w5m3f8b57a305c74ebe93087c4b0300eda4

What is FRAME_TYPE 20 doing for you if you have a + configuration?

I am not expert in the logs however you have a massive spike on both your magnetometers on the X component and this causes a lane switch from what I can tell. This would at least account for the altitude change. Given that the mag spike was on both magnetometers then I doubt there is a fault there but something has happened briefly to cause interference in the mag field. What it is I have no idea at the moment.

@dkemxr @Carapau thank you both for looking at the data, i was away from work so couldn’t reply.
@dkemxr the frame is a custom +, we had defined based on the motor weightages.

@Carapau our system doesn’t have compass, heading is sourced by dual GPS modules, can the magnetic interference still effect our system?
one doubt i had was there was a IMU switch at the time of the incident, and the altitude difference makes sense if i consider the altitude data from both the IMU’s, so my doubt is in what all conditions the IMU switching is possible?

Can you post your params file too?

Just extract the parameter file from the Flight Log posted.