Depends on the changes you think they've been making. There's a lot of stuff that can be changed server-side on any game which would be transparently replicated to clients.
For example, they could alter the Maximum HP value of Monster X, and the next time that monster respawns, it would use the new value instead of the old value. Spawn points, drop lists, can be altered like this too, etc. Small changes like those would not even require any altering of the server code at all, given decent coding.
Although, strictly speaking, although they CAN do this, developers generally will not. It's kinda risky to alter stuff on the fly without making sure it will work. A typo in the ID for an item in a monster's drop list could bring the whole server down next time that monster dies. Of course, it probably wouldn't, I'm sure people are better programmers than that, but you get the idea.
Also, generally speaking a "server" is usually made up of a "server farm", which you can think of as a single giant PC made up of 100's of processors. Each of the things in the game that need serving, run as a separate application on a single server. So the "Auction House" is an application, a particular zone has an application running it, when a group starts an instance raid, an application will be ran to handle it.
Because of that, it's possible to shut down only certain sections of the server at a time, such as shutting down the AH without having to boot anybody out of the game.
I'm not 100% sure on any of this, but I'm quite sure this is how any MMO is handled. Having a single "server application" per server would be an absolute mess.
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