You can use the delete command. https://docs.splunk.com/Documentation/Splunk/6.5.2/SearchReference/Delete
If you can write a search that limits the data to one copy, then you can pipe it to the delete command so you won't see both.
This will only stop you from seeing it, it will not get rid of the data off the indexer.
You can also clean indexes if one of the copies of data is in a different index than the other you can wipe one of the indexes of all the data in there. http://docs.splunk.com/Documentation/Splunk/6.5.2/Indexer/RemovedatafromSplunk#Remove_data_from_one_or_all_indexes
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