Cube black (3.6.9) with dual serial GPS (Here1 and Here2) not flown for ~6 months Alt Control Issues

DJI S1000 build with Cube Black and dual GPS (Here1 as GPS1, Here2 as GPS2 not CAN) had flown previously very well. Didn’t get flown since last December. Try to fly it the other day in the same configuration that flew fine before and it has serious altitude control issues in flight.

Have made sure aircraft is warmed up enought (brd temp set to 60) and power cycled before launch.
This exact same issue occurred on two almost identical 3.6.9 aircraft that had been sitting for the same amount of time with no hardware or software changes since the last successful flights.

Logs etc from AC1, Logs etc from AC2.
Tried updating one aircraft to Arducopter 4.0.3 and it resolved the altitude control issues but introduced very unpredictable compass issues (20% of boots work fine and flies as expected, 80% of boots have heading stuck at 0 degrees North and constant bad compass health/pos horiz variance)