Chests disappearing on upgrading world from 1.7.10 to 1.8

When our world on our server was upgraded from 1.7.10 to 1.8, I noticed that a lot of my chests were missing from my storage room. Parts of walls and the ceiling were missing as well. I have done some testing regarding the biome it's in and if it had anything to do with the obsidian or whatever, but alas.

Here is a video on the issue:
https://www.youtube.com/watch?v=_cA2hEj_61Q

Chests in other parts of the world have gone missing too, but not all of them.

The part mentioned in the video is located around:
X 321
Y 5
Z -317

Download (a part of) the world here:
https://www.dropbox.com/s/3yg84yrbxniaf0r/1_7_10.zip?dl=0