Let me start saying this issue is an older one and involves an extremely old world from beta 1.3 being updated to minecraft 1.12
I personally have no issues converting the world forward all the way until 1.7.10, then Mojang attacked... By changing all the block IDs.
What occurs is upon loading the world into 1.8 or higher, all chests disappear. Its a similar issue I had to some of the grass disappearing which was attributed to the weird meta data attached to it (non "0") but that was fixed by MCEditing all the grass.
I dont understand chests however since their data says their rotation so I dont know why they are being deleted upon loading of their chunk.
Any help would be appreciated. My nostalgia will thank you!