you should only have a single copy of the buckets from non-clustered splunk installs. we don't replicate your old pre-clustering buckets, so we don't expect there to be more than one copy (which is likely why the second peer wasn't allowed to add itself to the cluster).
if you want to make your old pre-clustering buckets clustered (and replicated), see
http://docs.splunk.com/Documentation/Splunk/6.4.2/Indexer/Migratenon-clusteredindexerstoaclusteredenvironment
https://answers.splunk.com/answers/106482/any-details-on-how-to-attempt-to-cluster-legacy-data-even-though-its-not-recommended.html
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