When changing to firmware upgrade mode, the EV3 changes its USB device ID (that’s why it appears as disconnected in the EV3 tool). So we just need to add a new USB filter rule in the VM settings:
0694:0006 "LEGO EV3 Firmware Update"
The original filter, for normal operating mode, is
0694:0005 "LEGO Group EV3"
And of course I made a video showing how to do it: