How can I discern which files in my public html folder are used by which domain?

I inherited two websites on the same host server and several thousand files/directories that are not being used by those websites. I want to remove those files that are not used. I have tried using developer tools on Chrome and looking at the network tab to see what is served to a browser when navigating to those websites but there some files that are never passed to the client. Does anyone know a way to do this efficiently?