It would appear that Apple have changed the way homescreen/standalone web apps work in iOS 6. According to various blog posts (example) these apps now get their own dedicated s
If the iOS6 device has a jailbreak applied, you can use ssh to delete the content of the folder "/private/var/mobile/Library/Caches/com.apple.webapp".
Next time that you start the web app, all files will be re-downloaded from the webserver.