When asked to switch from normal operation mode to firmware upgrade mode, most tools will perform a reset. This forces the tool to re-enumerate on the USB bus. The Virtualization software may fail to reattach after the re-enumeration, resulting in a disconnected tool.
Ordinary virtualization software supports the idea of USB filters where you set a collection of USB devices you want to automatically attach to a given guest operating system. Check the manual for your virtualization solution to see how to do this, or see the Firmware Upgrade Fails on VirtualBox.