Remove Replicated files on only one Server

In the past we replicated our files in two location. We are starting to run out of server space at one of our location and identified that since our 2 different locations are different divisions working on different projects we no longer needed to replicate certain folders in both locations.  Now that we have implemented this change I am looking to remove the files from the server that are not needed without losing database information on those files.  Has anyone tried to do this before and knows the proccess?

Thanks,

Adam

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