That's the thing--as far as Mettaton knows, there's no one left in the Underground. Apparently that wasn't the case for Alphys.

"Empress Undyne?" he repeats, raising an eyebrow. That's news to him, as is the barrier. That didn't exist anymore as far as he knew. Of course...of course things were different between them. "It seems we have a different set of memories, Alphys dear. I have no recollection of Undyne ever being the ruler of the Underground."