I have the very same issue, I was on a flight WSSS to RJAA. About 6-7 hours into the flight I get the same symptoms, low frames, low GPU usage.
When checking DEV mode the bottleneck were Main thread and Manipulators.
However one VERY strange thing I noticed this time which can indicate the issue. The moment I touched down the runway on landing (I mean the VERY moment) I regain all my frames and performance, back it was as smooth as butter.
It seems like something is bothering the sim while the plane is airborne.
I was also Flying 787 Heavy mod.