Magus' castle was destroyed by Lavos... Thats hardly a good comparision.
What/whos comparison are you referring to?
When they say Magus Castle they mean the continent where it was located.
Ok, alright. After consulting the maps, I've decided a couple things.
A) I was wrong about the Fair. In the 1000 map, the mountin is COMPLETELY GONE. Now THAT'S weird...
B) Dorino's mountin area shifted over more than I remember, but I stand with that.
C) I forgot about the Giant's Claw. That thing disappeared completely too.
D) About Magus' Castle: after the fight, the part of the island his castle was on is still around, and the cave you use to get to it is the same cave above Melchior in 1000 AD. Who knows where the upper part of the island went, unless the cave just shifted to the top of the island as the island moved down and connected with the Medina continent.