I don't see how Matt. The server has both FMS databases on, upgrade FMS in the normal way then just run DBUpgrade for the other one. When you are on the client machine with the two different shortcuts, as soon as you double click the client it will upgrade. When you use the 2nd FMS it will do the same.
Surely it is quicker to run DBUpgrade once more on the server and wait another minute for two local copies of FMS to upgrade than build a virtual machine with the time cost of creating the image with all of the updates of windows, the license cost for another OS, hard drive space, etc. FDS is good but the SIMS multiple connect.ini is better. Maybe Phil can put in a request to make FMSConnect.ini work like Connect.ini so one copy of FMS can have a drop down to pick which DB that they need. Surely with the increasing number of Academies there must be a demand as typically they need to see their old school's data plus their new Academy data. I am not a fan of FDS but it is usable. I don't think running DBUpgrade for a minute is hardly a upgrade nightmare.