How to Safetly Restart Your MySQL Slave Server

• Make sure that nothing can access it
  (take it off the load balancer).
• in mysql client do: STOP SLAVE;
• in mysql client do: FLUSH TABLES;
  (if it gets stuck here, then you might need to fix it. You can try UNLOCK TABLES.)
• in command line do: /etc/init.d/mysql stop

...do your what you need to do here...

• in command line do: /etc/init.d/mysql start
  (check for errors, sometimes in my.cnf)
• in mysql client do: START SLAVE;
  (normally this would be done automatically when you restart mysql)
• in mysql client do: SHOW SLAVE STATUS\G
  (check that replication is working properly)
• After you are satisfied, set up the slave server back on the load balancer