The latest revision of the SARA AFF boards have a 2nd usb connector.
On the earlier generations we only have the I/O holes.
You can solder on a usb cable to the SARA USB_DET, D+, D- and the ground wire to any of the available ground pins.
Put the passthrough on the microcontroller to turn on the module.
Connect both usb cables, now you should be able to load the latest ublox firmware.