Include a version number consisting of the timestamp of when the game was compiled. If the current version stored on the server is different from the cached version, the cached version should be deleted and redownloaded.
The app cache already does this. See http://www.scirra.com/tutorials/70/offline-games-in-construct-2
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Complaints that certain bugs weren't fixed with a game of mine indicates that somehow that function isn't supported with r144.2.