I’m getting the same thing with the added fun of having my Rift S disconnect at least once per flight. Been this way since the day I bought it and have found no solution.
But I have read somewhere that you should start VR in the menu right before starting the flight and don’t switch back. I think there is a bigger issue of as time progresses, the stutters and framerates get worse no matter what you do. A 5-hour flight would be impossible for me, especially in an airliner like PMDG. The frames would be so bad by arrival I would not be able to land. I can barely make a two hour flight.