Afraid not. Either you or the server will set itself up in install mode, which means that any user that is on at that point will also be using the server in install mode, IE BAD!
I understand it is not something that is wanted, but I only publish seamless applications to the users, so they do not have desktop access. Can it be done, or does it create problems???
Install all applications from the console, with no users logged in.
Make sure you use add/remove programs or change user /install.
Doing it any other way will cause problems. There is no other option unless you want to spend lots of $$$$$ to bring and expert in to fix it anyways.
Trust me from experience, staying late, doing it after hours or kicking everyone off the server for 20 minutes will more than save you time and money in the long run.
Also, if you have more than one server, just publish all your apps on the one server
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