The wiki said to cut the trace which turns out to be no easy feat. I did that and verified that the internal no longer working but I'm getting some odd random problems that make me think it's not a clean cut and it's popping in and out causing the APM to lock up while bench testing.
Can I simply remove the entire HMC5883L chip just to make sure or would removing that chip cause other problems?
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You can removed the whole chip if you want. That should not be a problem.