A patch https://patchwork.kernel.org/patch/10212201/ is going to fix
this issue properly, it should be backported to older kernels too, so
hopefully going forward your USB-C connectors will work correctly, it
also fixes NVMe drives disappearing after suspend too

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https://bugs.launchpad.net/bugs/1577898

Title:
  thunderbolt hotplug is broken

Status in linux package in Ubuntu:
  Fix Released
Status in linux source package in Trusty:
  Fix Released
Status in linux source package in Vivid:
  Fix Released
Status in linux source package in Wily:
  Fix Released
Status in linux source package in Xenial:
  Fix Released
Status in linux source package in Yakkety:
  Fix Released

Bug description:
  Thunderbolt hotplug is broken on type-c ports.  Redhat already
  submitted a patch for this that was accepted into upstream ACPICA, but
  it needs to be backported into Ubuntu's kernel.

  I've verified that the patch works properly using a type-C USB
  Ethernet dongle as well as hot-plugging a Dell TB15 dock.

  http://www.spinics.net/lists/linux-acpi/msg65578.html

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