Best I can offer is the "good" kernel logs:
[166187.229403] usb 2-1.2: GSM modem (1-port) converter now attached to ttyUSB0
[166214.856605] usb 2-1.2: USB disconnect, device number 52
[166214.856882] option1 ttyUSB0: GSM modem (1-port) converter now disconnected from ttyUSB0
[166214.856905] option 2-1.2:1.0: device disconnected
[166215.044609] usb 2-1.2: new high-speed USB device number 53 using xhci_hcd
[166215.134342] usb 2-1.2: New USB device found, idVendor=18d1, idProduct=d00d
[166215.134345] usb 2-1.2: New USB device strings: Mfr=1, Product=2, SerialNumber=3
[166215.134346] usb 2-1.2: Product: Android 2.0
[166215.134347] usb 2-1.2: Manufacturer: Androi
[166215.134348] usb 2-1.2: SerialNumber: 0123456789ABCDEF
Rather obviously these differ from the logs you posted so rather than worry about the fastboot tool I guess we have to focus on why the USB device did not re-enumerate.
I haven't got much of a clue about that except to say that hisi-idt.py isn't 100% reliable and that both the "GSM modem" mode and fastboot mode have timeouts (~60 seconds). However if the timeout is reached then the fastboot device should still show up on the dmesg logs.
PS Looking at some of my notes I think I still use the old 15.11 firmware on my CircuitCo Hikey. So, a long shot, but before giving up it might be worth trying with http://builds.96boards.org/releases/hikey/linaro/binaries/15.11/l-loader.bin instead.