See the Multitasking Enhancements and the silent push notifications in particular. Using the silent push you can notify your app that new content is available and also download that content and/or set the badge number for example without displaying the notification in the “Notification Center”. You’ll have to set the UIBackgroundModes with the remote-notification value in order to make this work.
You can send silent push if the user has seen the content on another platform and clear the badge number on your iOS app.