So an important thing to understand is that the cache management dashboard does not handle the /uploads folder, it handles the relay sha1 cache. Cleaning the relay cache does nothing for you – the relay cache rotates automatically and all you get out of manually cleanup is begging for cache thrashing.
What you seem to be looking for is a way to clean up the uploads directory – The upload manager service has a method for handling this but it isnt foolproof – as a result, C3 Platform Kickstart has some session relevance that can help you achieve this goal simply enable the Analysis, “BigFix Server - Uploads - Windows” in C3 Platform Kickstart and run the linked session relevance and it should provide a list of unused uploads.
As always when taking code from strangers do a spot check and make sure you’re not deleting anything that is important. Always backup the files first before deleting.
You can use this list in combination with a batch script or powershell script to clean out the uploads directory of unused files.