Hey,
We had thermal problems with USB. In our case, I can’t be sure it ever affected the controller itself.
The main problem for us was heat transferring back through the ports to some of the USB power supply chips on the other side that would get to hot and throw an over amp code back to the USB controller / OS and cause a sudden reset. This would happen so often the devices would take themselves offline. The annoying part was this only occurred when I put the lid on the cases.
We were using the onboard wifi as a connection, but when I tried to give them direct Ethernet access it wasn’t able to bring them back online.
See my post here for how we resolved our issue. I am not sure it would work in your case or if we are even having the same problem.
Good luck.
-Thomas