So after all the years I have been messing around with virtualisation I can confirm that 2 r9 290X crossfire in a windows VM without issue.
I know the tech is dated but I am getting closer to my goal of flexible and powerful distributed computing for my home.
I can also confirm that hot-unplugging 1 gpu does not cause any instability while crossfire is enabled.
I can now carry on writing my libvirt project to intelligently allocate resources for users requesting hardware for their VMs.