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The right way (tm) is to have the application deployed with high availability. That is every component should have more than one server serving it. Then you can take them offline for a reboot sequentially so that there's always a live one serving users.
This is taken to an extreme in cloud best practices where we don't even update any servers. We update the versions of the packages we want in some source code file. From that we build a new OS image contains the updated things along with the application that the server will run and it's ready to boot. Then in some sequence we kill server VMs running the old image and create news ones running the new. Finally the old VMs are deleted.