How do I ugrade BD when installing SP4 on server with DB on it also?

[mav1c]

I have a SD45 test server that has the Application Server and DB loaded together on the same machine. I upgraded the Server to SD45 Service Pack 4, so now I need to upgrade the existing DB. Problem is when going through the wizard, it prompts me to shutdwon the App server before continuing. I tried to just stop the app server, but I still get the prompt to shut down the app server. Is there anyway around this? Should I just continue with the DB upgrade and ignore the App Server shut down?