The original file(s) will not be deleted and the file set will keep its existing comments, likes, etc. To upload a new version of an existing file, please go back to the specific file's page and click Update File. This will create a whole new file set that can be commented on, liked, etc. To upload a new file, simply go to the specific page (be it a game, expansion, accessory, publisher, artist, etc) and click Add File.
