It's the third meaning, detecting a possible short. Also I think it's one of the ways the USB hardware detects a device change.
Anyway I now have a cable and have tried looking at the code. Fortunately it looks like everything needed for correct VBOF control is already in the hardware and software - the problem is that the Due circuit (incorrectly in my opinion) expects the VBOF signal to be active high, but the software is written for it to be active low.
I have been trying the following workaround: in loop(), immediately after the line usb.Task(); add the line uhd_set_vbof_active_high();
This seems to work most of the time but sometimes the USB device doesn't work properly straight away - try pressing reset, or disconnecting the device and reconnecting.
Can you try this and tell me if it works for you?