This issue occurred after updating one of these aircraft to 4.0.3 to resolve an altitude control issue. Alt control issue seems to be resolved 
Random bad compass health issues have replaced them 
Worth clarifying that sometimes (happened 3 times in a few hours of testing) the aircraft boots up just fine (still with the LED issues mentioned below) with good heading, no compass health warnings, and can fly auto missions and everything 100% normal. Power cycle the aircraft and all the issues are back. This behavior is shown in the tlog along with the normal flight log here. If I remember correct the normal flight happens at 60% of the log and then after landing the aircraft is power cycled and the heading and issues return.
Aircraft is an older DJI S1000 with Dual Serial GPS (currently Here1 and Here2 in GPS1 and 2 respectively). Had previously been flown on 3.6.9 without issue for some time.
On 4.0.3 now about 80% of the times the aircraft is booted it will snap to a heading of 0/359 degrees and then drift around randomly with Bad Compass Health and Error pos horiz variance and EKF Position (horiz) completely red.
Note: When powering on the aircraft both GPS units flash yellow initially, then only the Here1 in GPS1 does the red/blue initializing flash pattern. From then onwards the Here2 GPS2 unit LEDs don’t turn on at all. I expect the GPS2 LEDs to match the GPS1 LED pattern and color. This is concerning and my first course of action now that the aircraft is on 4.0.3 is to swap it over to UAVCAN and check/update its firmware. The GPS2 Here2 unit was purchased in July of 2019 and was only run on serial up to this point.