Are you experiencing AppCache error dialog that nags you to clear the Mobile Safari cache? But after doing so you still experience the appcache alerts/nags?
This is a known bug that appeared in iOS 4.X Mobile Safari that impacts all off-line webapps of any scale. We have invested a ton of time searching for workarounds to this issue, short of disabling the appcache support. Every quirk or exploit that we attempted only moved the problem to some other point that sucked as bad or worst than the current experience (major bummer).
To fully clear the iOS appcache users must:
1) clear the cache from the Safari settings
2) reboot the phone
The current practice is to either disable offline support or provide users with instructions for how to fully clear the cache.
See this Financial Times tech support page for an example of how one company assists users of its iOS mobile webapp:
http://apps.ft.com/ftwebapp/troubleshooting.html