This is a known problem for VMs, and each VM has different configuration, so it is not officially supported. The problem is that USB has to be configured to always pass through to the VM; flash involves USB disconnecting and reconnecting, but the VM is failing to reconnect. It can be made to work if you are able to configure the VM to always reconnect the Jetson, but flash software has no means of configuring the VM.
You’d be better off with dual boot of Ubuntu 18.04 if it is possible and if you cannot get the USB to not drop out in the VM.