I'm very interested in this question, as
Grok TiddlyWiki faces a similar problem moving forward -- users might want to update to the latest edition of the book, but presumably will not want to lose their progress in all of the takeaways. What I've done so far is load the takeaways (and the snippets) in shadow tiddlers, so if the user has personalized any of them, they won't change if a different version is imported (I imagine the easiest way to upgrade will actually be to export the takeaways from the old version and then import them into the new version, where the user's existing takeaways will hide any takeaways with the same ID in the new version, e.g., showing only the user's versions unless new takeaways have been added).
I could imagine extending this with a tool that identifies places where a shadow tiddler differs from an overridden tiddler, perhaps displaying the modification dates and a diff and providing the option of overwriting your version (or even just specific fields on your version -- e.g., in the takeaways scenario, the user might want to update the text of the prompt but keep the scheduling history).