Mary couldn't believe the man was floating above her. The world as she knew it had become upside down.
Meaning that everything Mary knew about the world was wrong.
Is the phrase a good fit here? If not, what's a better alternative?
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"Become upside down" is unusual here. The idiomatic phrase is "been turned upside down", though you will occasionally find "been flipped upside down".
Of course, the Fresh Prince of Bel-Air's "life got flipped turned upside down". It's never been clear to me whether his life was "flipped-turned" or whether his life "got flipped / got turned upside down". The latter makes more sense to me, but I always parsed it as the former.
"The world as she knew it had turned / had been turned upside down" is more appropriate though "had become" is not grammatically wrong. However, the idiom is usually used metaphorically for describing social upheavals or life-changing events, as in
"The war devastated the country and threw her life into chaos. They, who had been the richest in the city, found themselves in refugee camps fighting for their very existence. The world as she knew it had been turned upside down and she did not know how they would survive..."
John's infidelity turned his wife's world upside down.
I am not convinced 'a man floating above her' would "turn her world upside down" in quite the same sense as above; I think it becomes too literal here (rather than a metaphor) but it can possibly serve to suggest disbelief at the reversal of gravity and the alteration of reality. You need to be sure that you are using the idiom in an appropriate sense of the term.
I have read similar situations of unbelievable physical experiences in many science fiction / fantasy / horror novels. "She thought she was hallucinating", "reality turned on its head" and "sickening sense of disbelief" are some possible terms to describe the feeling. Some authors also write "she felt like Alice fallen down the rabbit hole" in reference to the the reality-distorting adventures of Alice in Wonderland.
The correct idiom is "world...turned upside down" from 1611 in the Authorized King James Version of the Bible. Speaking of Paul in the 1st century who preached the message of Jesus Christ's death and resurrection and all that it means to man. Acts 17:6 "...These that have turned the world upside down are come hither also;"