You can just leave the existing older versions online, or you have to actually regenerate each game manually.
On my SchoolHistory.co.uk and ReviseICT.co.uk sites I have made use of a custom dynamic system that I've developed meaning that there is one central game file that loads the individual topic data. However, it wasn't until I began developing my new site - http://www.icthistory.co.uk website that I've actually come up with what I consider to be the ideal solution.
What I've done is upload a custom version of each game. When the game loads, it looks at the url for two custom features - the type of game required and then the game topic. Thus, to play a Penalty Shootout game about the Amiga I just have to add that after the url:
Do try going to the custom page and experiment with the extensions. You'll be able to see how it is the same page that dynamically adapts to what you've chosen.
This might sound like quite an unimportant and mundane solution, but I do feel it can have revolutionary effects for those who have a range of games on their site.
If there is any interest I think I could turn this into some form of ContentGenerator Management System. This would include:
1. 'Data generator' program - producing the topic data files and allowing you to create your custom setup.
2. Dynamic versions of the programs to be uploaded to your website.
3. Help & directions how to set everything up
I think it would only be available to those who own at least one full suite - but I've found the solution to be extremely user friendly, so I'd like to gather any opinions. When a new update to a game is released, you'd just update one file and then every version on your site will be automatically updated.