In short, my team has a mobile site and an app in the appstore. We have added the meta tag to show the smart app banner. I saw it and everything worked as expected. Probl
There is a way to reset the smart banner behaviour without resetting all preferences. It requires either jailbreaking your iDevice or using an iTunes backup editor such as iExplorer.
/var/mobile/Applications/{Safari App ID}/Library/Webkit
(If you are using iFile, application names can be displayed along side the app id folder names. Enable Preferences -> File Manager -> Application Names
)
Browse Local iTunes Backups -> {Name of your iDevice} -> Backup Explorer -> AppDomain-com.apple.mobilesafari -> Library -> WebKit
(Disclaimer: I haven't tried this method because I use iExplorer in demo mode, which doesn't allow changes.)