The below story of joy was for naught. After the update the NIC port LEDs are solid, ifconfig status is “no carrier” and “I’m getting ix1: Error handling LASI interrupt -3”. Any suggestions are appreciated 
Bah, I thought to just shut it down while researching an answer so used “shutdown -h now” the last message was"ix1:link state changed to UP" It looks connected to my switch now but only after shutting down the OS ??? Anyone know what gives here ?
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Short story that probably won’t benefit anyone on losing a NIC and getting it back.
My Truenas Core 12 has been chugging away just fine until a couple of days ago. I went to to check the system as I figured it was finally time to move to 13. I saw I had no connection on my 10Gbe NIC (either port). I have a Supermicro X10SDV-4C-TLN2F. The IPMI port worked but nothing indicated a problem. I was also seeing LSI interrupt -3 faults. IFONFIG reported seeing the NICs but they were not attached. I did manage to get somewhat connected with a USB Ethernet adapter which didn’t work completely. I configured the system to use the USB with /etc/netcli, however When trying to connect to the web interface all I got was Truenas banner with “connecting” message then nothing over 8 hours (I went to bed).
I didn’t see anything to help online so contacted Supermicro who gave me some firmware to try. I booted up a USB LinuxMint live install I had and ran
the utility. It reported nothing detected to update. Even so, I saw the NIC LEDs were off compared to when TrueNAs was booted they were solid. I plugged into the top port and it worked ! Full speed, both ports.
I rebooted Truenas to see if I could work out how to update it and maybe a new kernel will have it working. I booted it, logged in my console and noticed the LEDs were off…!?! I plugged my cable in, and it connected. I readjusted the network configuration for the normal IP, rebooted and am now updating to Core 13 like the issue never happened.
Okay, I have no clue. I rebooted a few times, powered completely off a few times, otherwise booted once into a LinuxMint installation to run an Intel update that reported “nothing to see here”. Perhaps the act of booting or how the firmware utility communicated with the NIC triggered something to get it working.