If you are using CB3 JBOD control board, then it will be possible to do remote power down; If you use CB/CB2, then it’s not possible to power it in order.

Power down: Power off the system (with Avago controller) first. Then, remote power off the JBOD system.

Power up: Power up the JBOD systems first (remotely) and then power up the Avago initiator system.

Once when you do OS shut-down process, Avago driver and services will be turned off. Then, it’s fine for data writing back from cache to disk. Data will be OK.