Lost Continent, by Stephen Baxter
The short story can be found in the collection Phase Space, the companion to the Manifold series.
Two men are sitting in a café on Africa's northern coast, looking out over the Mediterranean Sea.
"It had been nearly twenty years since I had last seen Peter Dorehill, at our graduation together. Now, in the cool brightness of a café on Tangier's beach promenade, we sipped mint tea and appraised each other, as old acquaintances will."
They are discussing a theory about the fate of Atlantis. The theory is that Atlantis has been transported away by aliens and almost, but not quite, entirely removed from the collective memory of humanity. The aliens are said to do this whenever a unique culture is threatened in some way.
Atlantis is never mentioned. Dorehill speaks of his "lost continent" hypothesis and how it connects to widespread reports of earthquakes in the ring North Africa-Middle East-Russia-Scandinavia, at the time of the Cuban Missile Crisis.
Their talk turns to the Cuban missile crisis. This crisis might have endangered some unique cultures and compelled the aliens to step in to save them again.
Dorehill hypothesises that the Cuban Missile Crisis might have been a reason for aliens to safeguard lands (and the people and culture from it) threatened by nuclear annihilation. They would have had to physically remove those lands from Earth, and then remove any reference from the entire world's population's memory and any physical records to prevent the massive psychological trauma that the display of such immense powers would cause.
He also questions the necessity of the removal of the lands, if the Cuban Missile Crisis could have been solved without an all-out nuclear war.
Here there be spoilers!
The "unique culture" in question turns out to have been the entire continent of Europe.
Almost correct (see later). A clear hint that mainland Europe was removed is given early on in the story. Lvov is called a Russian port when in reality this is a city in western Ukraine, and is nowhere near open water.
... and the Mediterranean Sea stretches unbroken from Africa to the North Pole.
"I smiled. I stared out over the enormous greyness of the ocean - the huge misnamed Mediterranean, which stretches unbroken from North Africa to Scandinavia - and then I turned away and walked back into the bright, noisy clutter of Tangier."