To make a long story short, I tried to upgrade my SAS controller from an LSI 9307 to a 9400 series. I had the drives hooked up to the new controller, (which seems to have been defective) and the drives are no longer recognized by the controller. The drives do not even seem to spin up. I have other drives that spin up and are recognized by the same controller. Is it possible for a bad controller to make SAS drives (Ultrastar drives) unusable? Is there anything I can try to make the drives usable again?

Could the drives be waiting for a spin-up command from the controller?

Did you alter the power cabling? I don't know about SAS, but SATA has introduced a Power Disable feature on power pin #3.

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A backup a day keeps DR away.

I've tried covering pin 3, for the power disable fix. I have never seen something like this where all drives are no longer recognized.

Show us the component side of the PCB, or PCBs if there are different models. And please at least identify the model numbers.

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A backup a day keeps DR away.

The models are:

HGST HUH720000AL4200
Western Digital HUS728T8TAL5204

The drive may be waiting for a START STOP UNIT command:

https://documents.westerndigital.com/content/dam/doc-library/en_us/assets/public/western-digital/product/data-center-drives/ultrastar-dc-hc300-series/product-manual-ultrastar-dc-hc320-sas-oem-spec.pdf (page 227)

I know that SATA drives can be configured to power up in standby, so maybe that is also a feature of SAS?

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A backup a day keeps DR away.