When the issue happens, the server reboots into the EFI shell. When I go into the BIOS, The RAID controller does not show up. I install a replacement RAID controller (pulled from another server) into the failed server and everything is back to working.
The new firmware fixed the issue you are seeing.
Please refer to FAQ 42023 on how to flash firmware and delete nvram
https://www.supermicro.com/support/faqs/faq.cfm?faq=42023