Half a building missing, HELP!

[Blazerafe]

So whilst minding my own business not to long ago i had created the most awesome flying fort the world of minecraft has ever seen, or so i thought. I had set everything up including a nifty comet catcher and decided to see if i could use the rift to transport between two locations, i must have been gone a good 30 seconds and when i came back the once awesome fort now looked like this http://postimg.org/image/crwaa7vhp/ A giant square was taken out of the middle, that thing took me hours to create. So why has this happened and is there anything that can be done about this?