Seems like there is some work done in the 3.8-rc4 regarding xhci driver.

>From the changelog:
xhci: Handle HS bulk/ctrl endpoints that don't NAK.
USB: Handle auto-transition from hot to warm reset.
USB: Ignore xHCI Reset Device status.
USB: Allow USB 3.0 ports to be disabled.
USB: Increase reset timeout.
USB: Ignore port state until reset completes.
USB: Handle warm reset failure on empty port.
xhci: Avoid "dead ports", add roothub port polling.

After running for a couple of hours with this kernel the issue doesn't
seem to appear again, probably thanks to the "ignore xhci reset device
status" change.

There are events coming in the kernel log like "usb 11-1: reset
SuperSpeed USB device number 2 using xhci_hcd" but no disconnects occur.

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https://bugs.launchpad.net/bugs/1050352

Title:
  External USB 3.0 hard drive randomly disconnects and connects

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