Is this a quite big hybrid drone ? (THO is low, high current and no voltage dropping)
Firstly, high vibration on IMU 0 and 1, Vibrations are lover at IMU 2 than I suppose your vibration frequency is around 60-70 Hz. This is resonance value for pixhawk damping foam. To be sure you should do FFT analyze.
After FFT you should try some external dumping for pixhawk, if your copter weights more than 20 kg I advise you to add some extra weight for your pixhawk platform (around 100-150g) and use some soft dumpers. In my case, it gives great results.
I suppose the reason of EKF changing is high vibration even if you don’t have clipping.
Also if you have hybrid generator you should check mounting plate and isolate it from the frame. But firstly do FFT and publish it.
But here your vibe is quite high, I suggest to reduce it for around (15 max for z plus some extra shots max 25)
Also in your log i can see when you was flying go ahead on wind and with wind. Than you can check your frame maybe it is too lose or has to much space to bend. But also your tune looks good.