Mine is also virtual, so I will be making a snapshot!
So the correct procedure is ...
2. Update Ubuntu (hope it doesn't do something bad to ISPConfig's packages).
3. Update ISPConfig (hope that if the Ubuntu update did anything bad to ISPConfig that this fixes it).
I hate to say it, but my concern dates to the bad old days of applying a service pack to WinNT, where the service pack was likely to step on and break driver patches, so you had to do it in the right order and go back and re-fix stuff after applying it. I was worried that the Ubuntu update might patch the packages ISPConfig uses to versions that ISPConfig didn't like.