At some point when I was upgrading my server to the 1.9 snapshots I started to notice that a few certain chunks around my base were just up and reseting.
The chunks around my base were pre 1.7 which makes it really easy to see where the chunks are being reset because the are a completely different biome now.

It took me a while but I have found that the one thing that is in each of the chunks where this is occurring is a tamed cat. I went to another person's base where I remembered there also being a cat and sure enough, that exact chunk was also reset. I imagine that the issue with the cats is perhaps that they were tamed a while ago, possibly more than a year, because when I update the server and then tame a cat and then relog it doesn't delete the chunk. I also went back to 15w32c which is the snapshot before this issue occurred and I tamed a cat there and when I returned to the most recent snapshot it did not delete the chunks like it did with the older cats.