I'm running into a similar issue with an HP Zbook Studio G4 running
Ubuntu 18.04, HP Thunderbolt 3 dock and an IOGEAR 3.0/4 Port Peripheral
Sharing Switch (GUS434).  Often shortly after I switch back to the HP
using the USB switch I get the xHCI host controller not responding,
assume dead message.  Based on Oded's input above I created the
following service to fix it for me:

/lib/systemd/system/xhci-watch.service
```
[Unit]
Description=Restart xhci when it dies

[Service]
ExecStart=/path/to/restart-xhci.sh

[Install]
WantedBy=multi-user.target
```

script:
```
#!/bin/bash
dmesg -l err -w -T | awk -F " " '
        /xhci_hcd.*dead/ {
                system("sleep 1");
                device=substr($7, 1, length($7)-1);

                cmd="echo -n \""device"\" | tee 
/sys/bus/pci/drivers/xhci_hcd/unbind";
                system(cmd);

                system("sleep 1");

                cmd="echo -n \""device"\" | tee 
/sys/bus/pci/drivers/xhci_hcd/bind";
                system(cmd);

                notify="notify-send \"restarting "device" \"  \""$0"\" -u 
critical -i face-worried";
                system(notify);
         }'

```

obviously this is an ugly hack, but it might help some while a better
fix is developed.  My bash/awk skills are not the best, so please feel
free to offer suggestions for improvement

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https://bugs.launchpad.net/bugs/1766076

Title:
  USB over thunderbolt turns off every once in a while

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