What is the best way to handle this on BGG? Because BGG serves as an archive of all games (not just recent ones), it seems like files for the old version still belong on the website. However, confusions like this are bound to occur when rules change but the name of the game does not.
The best way to handle it is to properly name all file submissions. File submissions should always have version numbers associated with them. If the rules have a version number then that number should be part of the title for the file submission.