If an admin skin, and not a host skin, go under admin -> Pages, and check each page setting to make sure the skin is not being used there, such a possibly a hidden or disabled page.   Of course, check the site settings which is obvious (site defaults).   If you cannot find it used anywhere, and you have a default on the install still such as DNN blue skin, you can remove the skin folder from under the portal skins folder.   If a page was using the skin, it will then end up as the dnn blue default.

If a host skin, check each page for each portal, then be sure there is a default skin before removing files.
I would resync all files and double check all pages before doing something like removing a folder, but I have done it this way before without a problem.