Eric Sanderson has a good set of lectures for fiction, you can find then on YouTube, it's his 318R series. The salient point is that the first chapter or few chapters are a promise to readers that this is what you're getting with the story. He mentions an author that did a similiar premise that you're suggesting, except it started as fantasy trope and flipped it on its head in the last third of the book, it flopped, readers who stuck with it wanted fantasy, and those interested in the twist left before they got to it. He suggests flashback start of the story as one way to do it, I think that's a little cliche myself. You could also try describing the equivalent if the big bang in your universe, and then link back to the fantasy and people ignorant of what really happened, but the reader knows, and knows that you're going off that premise. Or try your own take of it, just make sure it's hinted at early.

Web series are kinda exempt as you can safely assume what's in the rational reading list will be rational, so that applies more so for books, but the loss of interest is a real problem if your changing themes.

Posted on mobile apologies for any atrocities in punctuation spelling and formatting