for what reason do you have one source multiple times? If that is due to compliance, stageing or data governance requirements you might have to go the hard way and install redundant storage instances (indexes).
If your architectures guarantees that all sources are the same at all time ... you just need to ingest one.
If splunk is used to verify that all sources contain exactly the same data you are free to choose for your source files. Put each in a separate index peer or index, or all in one and a scheduled search on top of that.
Hope that helps!