Setup will not try to copy any files if the folder /Data/Sites/[SiteID]/skins already exists, so its not going to fix it for you because that folder does exist. It seems it copied some of the files but not all of them. Please do what I suggested, use ftp and ensure all the files are there under /Data/Sites/1/skins, ie upload the skins folder beneath the /Data/Sites/[SiteID]/ overwrite any files that already exist, make sure there are no ftp transfer errors, retry until all the files make it.
Data/skins is just a catalog, the site uses skins from /Data/Sites/[SiteID]/skins
So if some files are missing just copy the catalog to the site using ftp to make sure all the skin files are there for the site.
Hope it helps,
Joe