Q:

What's the best way to shutdown one Citrix XenApp 6.5 server in a farm with users connected?

I have a citrix farm with four application servers. The users base connections are spread out over the four for load balancing. I want to shut one down for maintenance. Can I go ahead and do that without impacting the users? I'm assuming since the other three are still up, they will fail over to those for application use.

A:

No no - not correct at all. If you have a server, RDP/TS or Citrix XenApp (ICA) with active user sessions on it, and turn that server off, it will kill the sessions for those users and anything they haven't saved will be lost (depending on application.)
If they try to reconnect to the farm, and there are still servers that publish the application(s) they're connecting to, they will get a fresh session on a different server.
The typical way to do this is, way in advance, turn off "new sessions" on your server and wait for normal attrition (which will only be "normal" for your workplace's applications and users) to reduce the usercount to 0 on that server. Then, no one will be impacted when you bounce it.
For XenApp 6.5, this is in the AppCenter. Find the Server in question, right-click, Other Tasks, and pick the Prohibit Login option that best suits your needs. 
The other way, which can be combined with this way, is to have actual published/communicated maintenance windows during which users will know they're not supposed to be using the Citrix servers. Any remaining connections during this window can be killed, or depending on your workplace and the users, you could contact them and have them log off gracefully.

