First make sure that all your servers in the tree are communicating properly. Use DSTRACE on the servers in your network with the appropriate switches(+s,*h,+schema,*ss,+blink,*B, +j,*F,+agent). Run at server console.Make sure that the replica rings are in sync and communicating. Make certain that there are no unknown objects or obits(DSREPAIR -A). Also as said previously make sure that you don't have any Master replicas on the server you are removing and that all print queues and user files have been relocated. Make sur to do this after hours because there will be lots of NDS traffic as you delete.
Remove replicas one at a time from the server making certain that they have synchronized (DSTRACE switches) before you delete the next replica. When all replicas have been deleted from the server, you can proceed to removing volumes and licenses. Remember ro use NDSManager to remove the server itself. Check again on the remaining servers to make sure they have no communication with any objects associated with the 4.11 server. Once that is done you can safely power down the server. Check again in DSREPAIR on each of the servers to make sure everything is okay.