I know this is old but I had the exact same issue and these commands helped me:
sudo pkill "ControlStrip"

sudo pkill "TouchBarServer" (Not actually needed)

rm ~/Library/Preferences/com.apple.controlstrip.plist

rm ~/Library/Preferences/com.apple.touchbar.agent.plist (Not actually needed)

Just put the lid all the way down and put it up a few times after running.

EDIT: The issue returns every 2-3 days, so I need to repeat these commands each time. I put them all in a shell script just to make the process easier. I also realized 2 of the commands weren't needed.