I can boot either connected or not, and the first connection will
usually work.  I'd say my more common workflow is to boot away from my
dock, use my laptop for a bit, suspend, and go to my desk and resume
while docked.  That usually works, but if I then undock, use my laptop
for a bit, suspend, come back to my desk and resume, then I hit the PCI
issue.

I simulated that workflow and indeed reproduced the issue.  This morning I:
 - shut down my laptop
 - booted it while undocked (and captured dmesg and lspci)
 - suspended and connected the thunderbolt cable
 - resumed by pressing the power button on the dock
 - thunderbolt worked - captured dmesg and lspci again
 - unplugged the dock and captured dmesg and lspci while undocked
 - supended and connected thunderbolt again
 - hit the issue described in this bug - captured dmesg and lspci one more time

One mildly interesting thing is that while my system is in the final
"broken" state, lspci prints the following to stderr:

pcilib: Cannot open /sys/bus/pci/devices/0000:0b:00.0/config
lspci: Unable to read the standard configuration space header of device 
0000:0b:00.0

I will attach the dmesg as well as lspci I captured at various steps

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https://bugs.launchpad.net/bugs/1825395

Title:
  thunderbolt / PCIe hotplug gets confused after a few cycles on X1 Yoga
  2nd gen

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