Well i Think that the Cyrsta Empire wasn't "sent" in any place. It just doesn't exist anywhere during this about 1000 years. This time was for inhabitants like... well less than second. They all disappered and then appeared. Like they would been sent into future with whole empire(well one city is quite small empire, but still...). This would explain why they(I mean crystal ponies) are so confused and don't realize that this was 1000 years.

The only think I'm not sure is what happened with place itself - there where just empty buildings through this years? Or just empty space in places where were roads buildings etc. Or maybe there was some magic bubble which not allowed anypony to enter this terrains? Or send everypony to its opposite ends... or again to the point in which he passet it... I'm not sure what's the most likely.