Strange problem with APM 2.8 (clone) external compass

I’m using APM 2.8 with external compass (comes with GPS module M8N)
It was ok running external compass after I removed the jumper
But the problem caused after I tried to upgrade the hex file via Flip 3.4.7.
I can now calibrate by external module (to be able see the progress in Mission Planner)
But the quadcopter is using Internal compass to fly, Primary Flight Display immediately shows Bad Compass heath if I remove the external compass but this Display still updates Internal compass status,.
I don’t know why it calibrates by external but uses internal compass to fly.

Please give me an advice. Thanks