I had this happen too, after about 2 hours. I landed, i think i Alt-Tabbed out to check something in discord, when i came back i had no controls. Heli Manager didnt crash, but said “you must load a flyinside helicopter” with a Try Again button. Clicking Try Again did not recognize it. Then i tried quitting heli manager, same result. I had to exit the flight and respawn in. I also checked msfs sensitivity page in control options, the controls were properly recognized there.