I have had a similar - related issue.
While flying a Quadcopter - PixHawk AP, the Herlink GCS rebooted while the vehicle was in the process of returning to launch (in RTL).
The vehicle had been put in Loiter earlier in the flight (Chan 5 ~1500) before the RTL triggered from the HereLink screen.
With the vehicle a few feet from landing the HereLink finished rebooting (pinecone logo then QGroundControl)
The vehicle started flying towards the pilot and support and ended up upside-down in long grass - no damage.
Looking at the telemetry log the the AP i found the issue - as the HereLink powered up RC 5 went to 1100 - which changed the vehicle to Stabilise unexpectedly.
My suggestion would be that the RC controller part of the HerLink track it current RC output in non-volatile memory so that after a Reboot (not a controlled power cycle) it can power back up with the RC outputs tracking what they were just before the reboot.