In our environment we have percona cluster with 3 nodes and load balanced with HAProxy.
To correctly restart one node we need to mark the node as not accessible for application servers and just after there is no traffic, we can restart the Percona server.
HAProxy is checking node with xinetd services, so the easiest way how to mark not as not accessible is to stop xinetd service and than restart the mysql process.
Here is the command including sleep commands:
service xinetd stop; sleep 60; service mysql restart; sleep 10; service xinetd start
IMPORTANT: never try to restart 2 or more nodes at same time. Always restart node by node.