When the server was down, you shouldn't have deleted in from the tree in the manner that you did. How did you change the replica status? If you already had a Master and brought up this one with a Master then that will definitely mess things up. Remember 1 M and 2 R/W are minimum for a replica ring. If you are a good NDS troubleshooter this is still a tough problem. You can use the DSVIEW utility to find out why your OU is unknown and what attributes are missing. From there you can plan out your resolution to this problem. You need one healthy server in the replica ring that has all the objects from that OU. Find that server and make it the new master. Force a sync using DSTRACE commands. There are too many to list but you can find it on Novell's site. It sounds too late for that however.You may end up removing the server entirely and safely using NWadmin and NDSManager(Remove NDS from the server at the console). Wait for things to synchronize. You can force synchs with SET DSTRACE=ON SET DSTRACE=+S ,SET DSTRACE=*H SET DSTRACE=+BLINK SET DSTRACE=*B SET DSTRACE=+J SET DSTRACE=*F at the server. Using DSREPAIR -A at the server console, go to advanced options and check for external references. If you have anything other than 0 after waiting for a few minutes and they don't go away, then you have stuck obits and really messed up NDS. If you are not a CDE or at least an MCNE then call Novell.
If you get no errors then recreate the OU and wait for NDS to synch
then reinstall Directory services on the removed server and put the server in the newly recreated OU. Make sure you have licenses ready in case you need to reinstall. These are all NDS intensive tasks so you have to do it after hours. Once you have a version of NDS on your server you can use NDSManager to upgrade it to the latest from another server in the tree. Then you can play with replicas till you get what u want. Good Luck.