Same problem here: successfully connected my USB3 (Revoltec Case), but after some time, it disappears. This is reproduceable, and does not appear when connecting to a USB2 port.
THREE things seem to be reliable up to date:
1) There are manual "tricks" to reliably connect USB 3 cases
2) Those cases will reliably disappear within some hours or so
3) There is reliably none of the USB 3 cases from the reliably short qnap compatibility list available in "mainstream shops" in central europe
Sorry to all qnap people, I feel better now, and I KNOW you are working hard for it, but well, I bought a QNAP NAS advertised to be USB3-connective, and what I see is - by best effort - a "USB3 proof of concept"...