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Loss of altitude during auto mission

I was asked to help analyzing the altitude loss which occurs during auto missions with a copter.

The behavior happens again and again, it was not a one time event.
The copter is a 3DR Y6 Copter with Pixhawk and uBlox GPS.

LOG file and flight plan:

https://www.dropbox.com/sh/a37n0rq4gu3uwz2/AAAO8CXbzpJ6pGBhGxvXxtica?dl=0

I had a look, but can't spot anything (the altitude loss occurs at around 3.5 minutes).

- vibrations are ok
- RC/TX connection is ok
- no pilot input during this time
- GPS is ok
- all in auto mode during this time
- the mission is defined to be at a height of 200 meters, so there should be no loss of altitude
- the loss of altitude is visible in the LOG file
- desired altitude decreases (why??), this leads the copter to loose height

I am stuck with this one,
any help is appreciated

thanks a lot

Felix

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