Thanks for the logs. It seems like the BIOS does not handle S3 exit
properly and leaves the Thunderbolt host router unconfigured. I wonder
if there is a BIOS upgrade for this system and have you tried that?

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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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