There are two primary ways of doing this; 1) full restart or 2) rolling restart.

In the full restart case you can stage your updated code/configuration/etc..., stop all of the servers in the ensemble, switch code/configuration, and restart the ZooKeeper ensemble. If you do this programmatically (scripts typically, ie not by hand) the restart can be done on order of seconds. As a result the clients will lose connectivity to the ZooKeeper cluster during this time, however it looks to the clients just like a network partition. All existing client sessions are maintained and re-established as soon as the ZooKeeper ensemble comes back up. Obviously one drawback to this approach is that if you encounter any issues (it's always a good idea to test/stage these changes on a test harness) the cluster may be down for longer than expected.

The second option, preferable for many users, is to do a "rolling restart". In this case you upgrade one server in the ZooKeeper ensemble at a time; bring down the server, upgrade the code/configuration/etc..., then restart the server. The server will automatically rejoin the quorum, update it's internal state with the current ZK leader, and begin serving client sessions. As a result of doing a rolling restart, rather than a full restart, the administrator can monitor the ensemble as the upgrade progresses, perhaps rolling back if any issues are encountered.