I only play warbirds - P51, Spitfire and 109.
It happens with all of them randomly. Perfect example was with the Spitfire last time (I play in vr): Joystick hat no longer controlled trim, double throttle added to joystick which conflicted with actual throttle setting, throttle flaps weren't mapped, cockpit / map view not mapped to throttle. But other settings I had previously mapped were there.
I just did a full deinstall -> deleted DCS content folder -> reinstall. I will see if this changes things. Ugh... For a game that relies heavily on joystick mappings I would expect them to be handled more securely...