If I plan a mission for Auto Mode, will Auto mode override the settings set in GeoFence or should the fence be disabled or settings changed before flying a mission?
Thanks in advance
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Generally no, the geofence will take priority.
It does depend on the parameters your APM is using. See http://copter.ardupilot.com/wiki/arducopter-parameters/#FENCE__Para... for full details.
I should add that the flight modes are independent of the geofence system.
Great.
Thanks Stephen.