Chosen Solution

My Mac Pro 7,1 (2019) two top Thunderbolt ports do not work as either USB or Thunderbolt. They can however charge devices. My Pro XDR Display doesn’t work when plugged into the top ports, it only works with Apple I/O card. The system inspector only shows 1 Thunderbolt Bus

I reset the NVRAM and SMC to no effect. Does anyone have any ideas what the issue could be?

Take it to Apple and make them deal with it. It’s still under warranty plus parts aren’t available yet. Since the Apple stores are closed, it may be a case where you need the riser board that’s screwed into the case. I’ll work on the APN but that’s what the part looks like, but for now I’m stuck since nothing has leaked on this one yet.