Legacy stores have a "Files" button in the Yahoo! Store editor. This can be used to upload files to the store, things like pdf files, images, videos, whatever. It used to be that there was a separate "Files" library for the editor and for the published site - just like there is an editor version of your store and a published version. Well, apparently, there were some internal changes recently, and either this is not the case, or there is something with how Yahoo! Store resolves references to the file library.
The issue: if you have a file (say, image.gif) in the file library, and your store has been published, back in the editor if you upload a new version of this existing file with the same name and try to reference it (as /lib/yourstoreid/image.gif, for example), you will see the old, published version, no matter how hard you try. The only solution at this point is to upload the new file and republish the site. After that, you'll see the new version.