I found an additional reproduction case that does not require rebooting and 
suggests this may be related to host-side Thunderbolt PCIe/xHCI tunnel 
teardown/recreation rather than the HP dock specifically.
I tested a Dell WD19TB/WD19TBS Thunderbolt dock.
Boot Ubuntu with no dock attached.
Hot-plug the Dell dock.
Dell dock works normally, including USB keyboard/mouse.
Physically disconnect the Dell dock.
Physically connect the HP Thunderbolt Dock G2.
HP dock is detected and authorized, but its USB keyboard/mouse do not work.
The Dell hot-plug creates the following xHCI endpoint:
pci 0000:05:00.0: [8086:15f0] type 00 class 0x0c0330 PCIe Endpoint
xhci_hcd 0000:05:00.0: xHCI Host Controller
The Dell USB hierarchy then enumerates successfully, including the Logitech 
keyboard/mouse and Ethernet.
When the Dell is disconnected, dmesg reports:
thunderbolt 0-0:1.1: retimer disconnected
thunderbolt 0-1: device disconnected
When the HP G2 is subsequently connected:
thunderbolt 0-1: new device found, vendor=0xf0 device=0x467
thunderbolt 0-1: HP Thunderbolt Dock G2
thunderbolt 0-0:1.1: new retimer found, vendor=0x8087 device=0xd9c
However, I do not see a new PCI discovery/initialization sequence for 
0000:05:00.0 corresponding to the newly connected HP dock.
Eventually:
xhci_hcd 0000:05:00.0: xHCI host controller not responding, assume dead
xhci_hcd 0000:05:00.0: HC died; cleaning up
At this point boltctl list shows the Dell dock disconnected and the HP G2 
authorized at 40 Gb/s, but lspci still reports:
05:00.0 USB controller [0c03]:
Intel Corporation JHL7540 Thunderbolt 3 USB Controller
[Titan Ridge DD 2018] [8086:15f0]
The HP G2 previously identifies its xHCI endpoint as 8086:15ec.
I also confirmed that the Dell dock exhibits the original cold-boot problem: if 
connected during restart, its USB devices do not work; if hot-plugged after 
Ubuntu has booted, it works.
Thus the issue reproduces with Thunderbolt docks from two different vendors, 
and switching from a working hot-plugged Dell dock to the HP G2 can reproduce 
the failure without rebooting.


** Attachment added: "hot swat dell to G2.txt"
   
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/2163288/+attachment/5991852/+files/hot%20swat%20dell%20to%20G2.txt

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https://bugs.launchpad.net/bugs/2163288

Title:
  HP ZBook X G1i: JHL7540 xHCI dies when Thunderbolt Dock G2 is
  connected during boot; hot-plug works

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