The answer is: Yes , you can do it, and you can even do it well if you try hard and if you follow some basic "rules". Details below:
So, your story seems to need the kind of plot where the main character is reactive - that is, the plot is driven by the motivations of the antagonist, with the protagonist trying to foil his plan, instead of it being driven by something the protagonist wants to achieve and the villain is in his way. This is very important to remember from the first page, as it will set the tone of your story.
You need to make absolutely clear to the reader, early on, that the stakes include a reality shift. This is not something you can shoot at them out of the blue. To do this effectively you will probably have to devote a decent portion of the first third of your story to explore the villain's perspective - what they want to accomplish, why, how etc. Needless to say, it also needs to be shown that they have strong chances of succeeding. A one-in-a-million shot that succeeds works if it's made by the hero - if it's made by the villain, it just feels lame. And you need to give enough hints that this will happen quickly - you can't mislead the readers into thinking this is your endgame , you need to convince them that the conflict to decide the outcome of the reality-shifting plan is only the first major climax in your book and it is coming soon. How you accomplish this is up to you.
Because the antagonist will succeed, you will have to try and make them rather sympathetic to the reader , so that they feel that even if they accomplish their objective, maybe not everything is bad. An entirely unsympathetic villain cannot work well with this.
Now you approach the first climax point at the 1/3 mark. Hopefully you've built up reasonable tension, a plausible explanation for the mechanics of the reality shift, and shown that your villain is capable of and determined to go through with it, while your hero is trying to stop him. How the conflict is managed will depend on your story entirely, whether it will be a physical battle with swords, a duel of magic, a chess game for control of a supercomputer, whatever. However it needs to be desperate for both sides, it needs to push both to the limits , if the villain accomplishes his goal too easily here, then the entire story falls apart. The readers need to be convinced that the reality shift can and will probably work, but at the same time they need to believe that it can be prevented until the very last second. In a way, for this part, your villain becomes your hero - much like, during the climax of a conventional (good) book, the reader pretty much knows the hero will win, but is on the edge of his seat to find out how, here you need to do the same for your villain, so that when the reality shift happens, it feels like a satisfying, deserved victory rather than the villain trolling the hero.
BONUS POINTS : at the end of the struggle, you leave it unclear who won and who lost. Then you jump to the "normal" world post-aftermath, and you spend maybe a chapter of ambiguity dropping hints that something is not right, but leaving it to the reader to try and figure out if the reality shift happened or not. However this needs to be resolved fairly quickly, I'd say one chapter at most, before you confirm.
All of the above was the easy part. Now we actually get to the part that requires effort.
So the reality shift happens. The next step is to project your endgame to the reader. Your protagonist is in a new world that has been altered to the villain's image. Now I'm gonna pause and say that even though the details of the reality shift are up to you, you should follow some general guidelines:
1) The villain should not have had "absolute" control over what was changed. Otherwise it would be too easy for him to just ensure everything goes his way for the rest of the story. Whether you accomplish this due to limitations in the reality shift method, or some mental weakness of the villain, or any one of other numerous ways, is up to you. At any rate, you need to establish that either the shift was, from the beginning, a "general guidelines" sort of shift where the villain gave some directions but the details were left to chance/the internal workings of your world, or alternatively that the shift was only partially successful, preferably due to the hero's efforts. This is the preferred way in my opinion: the villain's plot was accomplished, but the hero's efforts opened a vulnerability that will be exploited later.
2) The "new world" is still recognizable as a shifted version of the old one. You seem to already be aware of this by what you wrote in the question, but it is very important to stress out. The changes must be small and subtle, and they must be MEANINGFUL. If you cannot put forward a reason for something to change, do not have it change (this doesn't mean you have to explain to the reader every little change, but you should be able to justify it to yourself). On top of that, if there are things that make sense to have been changed, you need to show them change. Otherwise you will come off as lazy. Internal consistency is a must.
3) The "new world" must not be all bad. This ties in with the need to make your villain sympathetic. You should show some positive outcomes from the change. That way readers actually become invested in the debate of which world is better and can find arguments for both sides, perhaps leading to an outcome that does not involve the world getting back to normal - instead maybe a compromise is reached between the old and the new. If you just make a crapshoot world, then the only desirable endgame is a full reset, which just makes for a bad story.
With that out of the way, the endgame. There are obviously dozens of ways to end this, but I will outline three main routes here, which along with the multiple variations should cover a large spectrum of possibilities:
1) The hero realizes the truth, then fights the villain for control of the reality-shifting power, then uses it to put the world back to normal. BORING. DO NOT DO THIS.
2) The hero realizes the truth, however the change is not reversible , whether due to the reality shifting whatever breaking or being a one-time thing or other cause. They try to work from within the new world to improve it, culminating in a battle of ideals with the villain. In the end the hero wins, the villain realizes the errors in his decisions (or dies I guess if you really want to) and they try to improve the new world internally.
3) The hero realizes the truth, then fights the villain for control of the reality-shifting power. However, as he is about to use it to put the world back to normal, he realizes this is not the best idea. Maybe he cannot directly undo the villain's work, and so if he tries to change the world, it would be changed according to his own image, which is just like what the villain did. Maybe what would be lost in the change, or the sacrifice to power the shift, is more than he is willing to pay. Maybe he realizes that the new world may be different from the old one, but that not all is bad, and that this world is also worth preserving. So in the end, he doesn't go through with the reset. What happens from there on is up to you, maybe like in 2) they try to work inside the new world, maybe something else. This is interesting and allows you to explore different facets of your characters, your world, and even play around with the definition of "reality". I personally would go for an option within this bracket.
Determining which ending you will go for at this point (if not earlier) is crucial because you have to build up to it. Each of the above variations will require completely different story writing in the remaining two-thirds of the book (and very likely even the first part, which may lead to rewriting - but that always happens)
So now you are 1/3 in your book, and you have the ending defined. The next step is to sell your endgame to the readers. Do not leave too much ambiguity at this point, pick a line and go with it. If you build towards a reset outcome (1) only to reveal in the end that the thingy is broken and the only option is (2), it's crap. Like in the first part you can make it work, as long as you are honest to your readers.
What comes next? The next part should be the conflict between new and old. The hero needs to gradually work out the fact that reality has shifted, he needs to remember (part of) what has changed, and needs to figure out a plan to undo/mitigate/correct it. Here is where you will need to pull on the stuff that happened in the first third of the story. Almost everything noticeable that happened in the first third (old world) needs to play some part in the second third and help the hero realize the shift and/or help him figure out how to proceed. Again implementation is story-specific and up to you. This is where the other answers fall short: it's not like you are throwing the first third of your book in the trash bin. Rather, you are ensuring that everything the reader read about in the first third is so significant, that it guides the course of events even after the whole world has changed. Of course I'm not gonna get scienc-y here about this because the what how why depends extensively on your setting. A hard-ish sci-fi novel will have completely different rules and mechanics for the reality shift compared to a high fantasy one, or a psychological horror story.
And so we reach the 2/3 mark of the book, which should be another climax. What kind of climax? One option is to build upon the new vs old debate. After realizing the shift, the hero needs to face a deep internal conflict where his very reasons and resolve for fighting the villain are challenged. What if in the new world, he was able to find true love? What if his family which died when he was young in the old world, is alive and well in this one? What if the world is at peace? Does he still want to fight the villain and undo his work? Maybe the villain was right after all?
Now, here is a major catch. Can you answer "yes" here? It may seem like you legitimately can, depending on your endgame. But there is a caveat. If the hero accepts that the villain was right, then that means that the hero's struggle in the first third of the book was misguided, and his efforts are invalidated. And this leads to a bad story which other answers have alluded to. No, you need to convince the reader that despite the arguments in favor the new world, in the end, either:
1) The change was bad and needs to be undone (Endgame 1). If you followed my advice and made the villain sympathetic and his new world better in some aspects than the old one, this is tricky to pull off well. Why? Maybe there is a moral reason why the "old world" was the "right" one and changing it was wrong or had unintended consequences. But that feels rather shitty to the reader. Maybe the villain himself realizes he messed up and wants to undo it but he can't (or won't, if he cannot bring himself to admit his own failure). Either way it's hard but not impossible
2) The change had good and bad aspects, but the hero still wants to undo it (Endgame 2). This is where you can potentially play with the hero trying to undo the change, only to discover a while later that it cannot be done, and instead shift to them trying to work with/improve the new world.
3) The change had good and bad aspects. The way forward is not to change the world, either because the hero can't (Endgame 2) or realizes he shouldn't or doesn't want to (Endgame 3). Alternatively you can have the hero still try to move forward with a reset plan, only later to realize it is the wrong choice (Endgame 3) however that is trickier to pull off because hitting the hero with the "you were wrong" right at the endgame is a common place where writers trip - it can be done well, but it is easy to do wrong, and if you do it it's a great way to turn readers off right at the most critical part of your story. I would not recommend it and instead go with the more straightforward way of having the hero's plan be defined earlier.
Once you are done with this and have resolved your hero's internal struggle, you can move forward with the final confrontation with the villain and your Endgame.
TLDR : Yes, it can be done, it is a story like any other. It needs effort and hard work, just like any other plot. It can be good or bad depending on how you handle it. It's not even a really hard hook, compared to others.
Disclaimer : Above I gave some general guidelines on how to make this kind of story work. They are by no means absolute or all-inclusive, I just outlined a few methods I think most writers should be able to follow fairly successfully.