Just wanted to update on the issue. I figured out the setting AHRS_OPTIONS to 1 (which disables fallback to DCM in case of EKF error) will stop the autopilot from giving really inaccurate velocities and position when it loses satellite signal. However, I am still not sure why the GPS would spike randomly down to 0 satellites from 17. I also realized that my GPA.Delta would consistently spike to 220-240ms which exceeds the max refresh rate of ArduPlane so this may be a cause but I have no idea how to fix it.
Similar problem https://discuss.ardupilot.org/t/the-conversion-of-dcm-to-ekf3-caused-the-crash/105342/2