app.pane.history is not deprecated; it was a private field, which has never been a documented feature. Modifying internal and undocumented members of the Kendo UI framework is not supported.
Apart from that, the behavior you describe (iOS resetting the app state) is not specific to web clips. This document
describes the iOS apps state transitions in details.
If your only concern is the back button not working, you may hard-code a href attribute (and a reverse transition) for it. This his how our online mobile examples work, so that we may support deep linking to a specific example.
Saving and restoring the app history is not possible - the mobile application (and Kendo UI routing) relies on the browser history object navigation/events. The browser history can't be read or modified, due to security restrictions.
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