So - letting it unplugged didn’t work. Here is what I did to get it to work:
- Reset BIOS to defaults => didn’t help.
- Tried using ports 2 and 5 => Gave me partial success. No display and no ethernet though.
What happened was that the USB bus was constantly reset → Very annoying when listening to music.
Decided to revert back to a signed kernel → HWE kerne 6.8.0-40-generic and clear the UEFI keys and restore the official ones.
It still didn’t work. Status was still disconnected.
I then decided to test one last thing: Use USB-C on USB Port 1 instead of 4, plugging in while the computer was booted (up and running).
This seems to have reset the Dock. I could finally plug it into USB Port 4 again and thunderbolt was again usable.
To be honest, I have no idea what happened! But what an epic endeavour to get it working again.