Because I do not want someone to have to go through the trouble I did, I’ll document my journey.
I bought an LSI/Broadcom 9400-16i off eBay. I installed it in the same PCIe slot as my previous HBA and cabled it identically. Success! Until I looked at the TrueNAS storage tab and saw I had 12 unassigned drives. I posted here. I knew that was an answer, but I hated the idea of having a cable in my machine that didn’t go anywhere. My OCD was front and center. I tried a bunch of different things to get this to work, including moving cables around. Nothing.
The next day, after a set of fresh eyes, I realized the firmware on the 9400 was ancient. Of course, all my thumb drives were USB-A and my USB-C to USB-A adapter was at work.
Come home today, put the new FW on a thumb drive, realize EFI doesn’t support ExFAT, reformat the USB drive, and re-flash the HBA to version 24.0.0.0, boot up TrueNAS.. and still had 12 unassigned drives. WTAF?
I fumble around for 2 hours trying to figure out what the hell is going on. Of course, server machines don’t boot quickly, but at least I have IPMI so I can do most of the work from my lounge chair! Anyway, I went back downstairs to unplug one of the cables and resume my investigation tomorrow, and I noticed my expander was on P1 and P2, NOT P0 and P1.
So, if you have duplicate drives in your system, make sure your firmware is up to date, and make sure your expander is plugged into ports P0 and P1 or P2 and P3. Don’t be like me!
Thank for everyone here who helped guide me in the right direction.