I was playing survival mode, flat, 0.9.5. A little history. A few months ago, I placed a nether reactor over my house and it created a huge nether fortress on top of my house. Today, I logged into my world and found that my map had been completely changed!!!!! There may be no correlation between the nether core and what happened, but I thought I'd mention.
Today, I found that my house had been removed and replaced with a huge forrest. The mine beneath my house was gone and the ladder heading down to the bedrock was gone also. However, the mining down at the bedrock level was very large, so I had another mine entrance that was not altered. The mine was gone at the bedrock level beneath the forest that was placed above ground. Basically everything was replace all the way down to the bedrock level.
I had a lot of above ground buildings built and a large pyramid that were not altered. But I think that every storage box I had was gone, about 20 of them.
So, basically, my house was wiped out and replaced with a forest going all the way down to the bedrock level. All of this happened beneath where I had placed the nether core a few months prior.