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Source: https://writers.stackexchange.com/a/48673
License name: CC BY-SA 4.0
License URL: https://creativecommons.org/licenses/by-sa/4.0/

I would say that two things are essential to make your proposed reality-shift such that the reader doesn't feel cheated, and like they wasted their time. And I truly believe _both_ are essential, not either or:

1. Make sure that the potential for this outcome is expected, to some degree, before it happens. It shouldn't be out of the blue. That doesn't mean you have to telegraph it blatantly, such that it becomes predictable. Only that the reader should understand that the very reality which they are reading is at stake, and may not be preserved. 
2. Don't let _any_ of the events in the first 1/3 of the book be meaningless or irrelevant to the story. It might be a little strong to claim that none of them should be irrelevant, but this is just a good general rule of storytelling. Note, this doesn't mean that all the events that _ever_ took place during the first 1/3 of the book must be relevant, only that the events that took place _on page_ must be relevant. Any irrelevant events must be alluded to off-page. Depending on the rules of your world, relevance of events doesn't necessarily have to hinge on them having left any trace in history or people's memories. It just has to leave _some_ trace, whether it's by natural means or not. If you're contriving your story in such a way that _all possible traces_ that an event can leave vanishes (from the state of the world, the state of people's memories, other parallel worlds, etc), then you're rigging it so that those events couldn't possibly have been relevant. 

There may be no _natural_ means by which you can follow point #2 and still go the route you want to go. But that doesn't mean there's no _conceivable_ means by which this can be accomplished. You must simply have different rules in your world, which means you have a world-building task ahead of you. If you truly _can't_ find a way to accomplish this, then you may want to consider starting your story _after_ the reality-shifting event. (Although, if this is truly the case, I'd find it hard to argue that anything even _happened_ before the event, or that _before the event_ is even a coherent concept. If a tree falls, etc.)

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