Volume "Disappeared" After Improper Shutdown

[ere109]

This blog gave me significant hope: https://www.bussink.ch/?tag=sas2flash.
The writer has my exact motherboard, and says, "I have found that the LSI HBA 2308 on the motherboard had a tendency to drop all the Drives and SSDs under heavy I/O load."
I'm gathering my tools on the table, and will absolutely open the case, disconnect those drives and attach them to the motherboard ports, then run a few things and update the HBA firmware.

 

[m0nkey_]

I believe you both. Last night, I restarted the machine for the third or fourth time, and all of my disks and pools were back online! Definitely an odd series of events, and it gives me a lot more to scratch my head about.

That definitely a failing HBA.

 

[ere109]

That definitely a failing HBA.

Perhaps, but it turns out it's my only option at present. It's an on-board controller - not an add-on card - and when I opened the machine today I discovered that I don't have enough remaining ports on the native controller - 8 SATA drives and only six ports. So I disconnected all hard drives, powered up and updated to FW 20, then shut down and reconnected. As of now, the system is up and all drives are connected - I just won't breathe on it. I thank you both for your help. If I get another problem of any kind, I'll know exactly what the problem is and RMA the mobo and/or look for a replacement HBA.

 

[ere109]

UPDATE: First, thank you both, @m0nkey_ and @DrKK . You gave me the right advice. This afternoon I opened my case, disconnected all drives connected to the LSI 2308, and plugged the most vital six back into the main ATA controller. The machine booted happily, my main ZFS data store appeared and I've been able to access it all evening. Everything works again - and no hard drive errors to date.
I knew you were right, all along, but hoped you weren't. After firmware, I bought a new set of SATA cables, re-installed FN, and did everything I could to avoid finding out the truth - that my motherboard HBA was fried. When you put so many hours into building something, the last thing you want to hear is that you've got to tear it all apart and build it again.
I've put an RMA in with SuperMicro (the mobo is 6 months old), and hope they'll come through without any issues. I've also done some looking around online for replacements, but I'll wait to see what they have to say before I proceed.
I really appreciate your help, and the help of the community at large. This has been such a steep learning curve and I am so happy to have such a helpful community to turn to.

 

[DrKK]

It is our pleasure to serve you sir.

 

[ere109]

Further update, if you'd like to dig this old thread back up:
I sent the motherboard in to SuperMicro about a month ago. They tested it and sent it back saying the LSI 2308 showed no problems under multiple OS's. Tonight I played a game of cold swap, shutting down the system, swapping sata cables between the two onboard controllers, then booting into FN. Every time, the drives connected to the HBA were missing or disappeared shortly after boot - both zfs pool drives, random platter discs and an SSD. I'm planning to call SuperMicro tomorrow to discuss, but I may need to test with a few spare OS's to make sure it's not something with the FN driver. I wonder if they even tested it. This has been a long and frustrating road.