The two cities that were Enki's birthplace and adopted home in Eorzea technically
were destroyed completely, in the original timeline anyway - SHB's main scenario specifically showed Rhalgr's Reach - as in, Ala Mhigo, and Gridania being the two places Black Rose was unleashed by the Garlean Empire with destructive consequences during the future 8th Calamity virtually wiping their populations out wholesale in days (and from there, the rest of Eorzea soon followed, with the entire world collapsing into complete barbarism, even
the Empire that caused it). My character head-canon story wise was born in Ala Mhigo and started her adventurer journey both before and after the 7th Calamity in Gridania, so it was particularly gut-wrenching and horrifying to see on screen.
And of course the real kick in the gut with studded sabatons was that the
player's character was also a victim too and was killed during it. SHB's whole plot is a result of the survivors of the disaster trying to change history by saving the player's character from this fate. It's the reason for my
Heroes-inspired statement in my sig.