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Thunderbolt lost on ProArt B550-CREATOR

Level 7

I built a new system roughly 4 months ago and everything was working perfectly, until a week ago my system updated and the BIOS went to 3202 and now my Thunderbolt ports are completely useless. 

I've tried everything to rectify it to no avail. I've rolled back the BIOs firmware to 3002, 2803. I've updated all drivers from the ASUS support page (the Thunderbolt driver won't run though) and I've done a clean installation of Windows but nothing is working. 

The Thunderbolt control center driver is showing as 1.41.1193.0 with NVM firmware version 31.0

I've read that there is a thing about using all PCIe lanes however I am just using the one and I've had this working perfectly until a week ago with no hardware change. I also have the GPU plugged into the MB via the display port. 

I emailed ASUS a week ago and I've heard nothing and I'm not totally lost as I can't use the machine due to having an Apple Studio Display which only uses Thunderbolt.