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Can you make Splunk treat lookup files as local configuration?

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I am running a custom app that uses lookup files to get some of its configuration on a search head cluster. When the lookup files are edited on a search head they replicate across to the others with no trouble. Today I pushed some new configuration out using the deployer for a different app and the deployer has overwritten the lookup files that had been updated on the search heads with the original files that were stored in the deployer. Is there a way to make splunk treat the lookup files as local configuration? I assume that if I remove the original lookup files from the deployer it will overwrite the SH ones with an empty folder when I push out the budle. is that correct or will it only replace the files that it has an update for and leave the rest? Thanks

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