After more than a year with the navio I can assure you pulling the battery after a flight does not corrupt the SD card. Not that this is a resolution to your problem, but it’s one less thing to worry about… 
I first built my quad in November using whatever the default images and APM binaries were at the time.
I never experienced any problems with Mag or compass at the time.
I then relocated and had to break it down for packing.
I rebuilt it a few weeks ago using the latest image and latest release APM but with exactly the same hardware.
I experienced a number of differences.
The first was that the Wingle was no longer automatically recognised and nor were any of my usb wifi devices which previously worked fine.
The second was that I suddenly had Mag and compass errors. This was despite an exact rebuild of what I had previously in terms of the hardware and physical components (wiring and layout etc).
I then followed the Doc to upgrade the default apm.deb to the beta version.
My first attempt was not successful as I had errors with the apt upgrading process (libc).
I installed a new clean image and that resolved the issue. I assumed a corrupt image or failing disk at the time. But in hindsight I am not convinced that this was the case.
The second installation went according to plan. This solved the Mag & compass errors with no other intervention but has introduced other issues.
I recently I upgraded the operating system (sudo apt update && sudo apt upgrade) as a matter of course and while noticing that the previously missing wifi drivers were installed I also received a spurious error about a missing linux image.
I really believe that the issues we are experiencing are software induced. This is not a criticism or gripe just an observation which I hope will assist to solve the issues.
What is still not clear to me is how the apt update management distinguishes between the Navio+ and the Navio2 or whether there is even a difference. I believe that there is a difference because George points to two separate locations in the thread which describes how to upgrade to to the beta version for Navio+.
I agree… It looks like they had a wrong link to the kernel image. My guess is the pull request into ardupilot 3.4rc1 never got done.
Dale
Guys, this thread got impossible to manage. I closed this one and encourage you to either open new or post in the less cluttered existing ones. Thanks.