Vibration when using engine brake with full battery

Yes, the engine is run up to max RPM for maximum engine braking and it does make some noise and vibrate a bit. It won't harm anything. There is no fuel being injected during engine braking so the actual compression forces are quite low. The funny part of this is during the engine braking, if you press on the accelerator even a bit, the engine will -slow down-. Something you don't normally expect.

 

Already got used to how quiet & smooth the Prius normally is, eh?

That sound & feel is a bit out of the ordinary, especially for those of us who rarely ever see a full battery. But it is nothing to worry about. When it does that while your not moving, it's quite the reminder of how smart the system is... going out of it's way to maintain good battery health (spinning off excess charge) without you having to do anything.
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Scary the first time but normal.

 

Why would simple engine braking cause any vibration not felt in normal driving ?

If anything, running an ICE at the same rpm as when engine braking should have a higher NVH.