You should normally remove only duplicates AFCAD coming from *other* products (usually AI traffic packages), some of our sceneries have two and in some cases three AFCADs (JFK has a separate file for Approaches), and some are put into the Scenery\World\Scenery folder, when there's a need to change altitude compared to the default scenery.
If you are not sure what to remove, it's best to Uninstall our scenery first, then scan for duplicates, remove them, and reinstall our scenery.