Trying to follow the document.... which file do you have to manually update with the new index?
Splunkhome/etc/master-apps/_cluster/local/(server.conf) sorry I ment indexes.conf on the master node?
Then reapply the cluster?
Sorry, I was asking Steve G., I am having the same issue. I have added the indexes there and it pushes out the other indexes, but does not show on the deployment server under indexing cluster page.
as i read from document you have first to send data to newly created indexes in order to see them
You create indexes in indexes.conf, not server.conf. You update the file on the master node and then use the CLI command 'splunk apply cluster-bundle' to deploy the updates to the peer nodes.
For details on updating configurations via that command, see: http://docs.splunk.com/Documentation/Splunk/6.3.1/Indexer/Updatepeerconfigurations
(referenced from the 'configure peer indexes' topic as well)