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.
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It affects all snapshots past 15w32c. No option to select that range that I could see.

I can't seem to reproduce the issue. Please answer these questions:
Which version were the affected chunks generated in?
Which version were the cats spawned and tamed in?
Which version was the world last opened in before opening it in a snapshot?
Can you please attach the affected world (with chunks not yet reset) as well as a set of coordinates with tamed cats? Can you provide a step by step guide on how to reproduce the issue? Something like this:
1. Create world in 1.8.8
2. Tame a cat
3. Open world in 15w40b
4. Look at where the cats were

The chunks were generated in mid 2012.
The cat at my friend's base was tamed in late February 2013. The ones at my base were tamed much earlier than that.
We usually update to the snapshots as soon as they are available. During 1.9 however we had to stop when I noticed that chunks around my base were acting up. This happened right after 15w32c. We've stayed on 15w32c ever since. I check each new snapshot but the problem stayed with each update.
There were not too many cats so I just went around and killed them to prevent them from causing issues. I did notice that for some reason they were no longer responsive to me as their master meaning that I could no longer get them to sit or stand. It's possible that these cats are somehow corrupted and that is the issue here. I went to a newer member's base and their cats are fine. It must be something to do with my cats losing their owner or something. As far as I'm concerned this issue is resolved by getting rid of the cats before updating.
I am having a hard time getting the file size low enough to be able to send the world as an attached file so I have uploaded it to a dropbox account so that you can download it with this link:
https://www.dropbox.com/s/1btc9gt83iux68t/Archive.zip?dl=0
I moved the spawnpoint right near where one of the troublesome cats are (Near 0x 80y -3275z in case there are any issues). If you log in with 15w32c you will clearly see the orange cat hanging out near a fountain. If you then log in again with any snapshot past that point you will see that the chunk where the cat was is now reset and is a desert.
This issue is probably not one that needs to be worried about because it would appear that the cats are corrupt in some way but the file is there in case you want to check it out and try and find out what broke the cats or something.
Please let me know when you have the file so I can safely remove it from the dropbox. Thanks!

Got the file. I'll take a look in the evening.

Searge fixed it before I could take a look. Oh well.

I've been experiencing an issue of chunks resetting for a long time now. I hardly use snapshots, but it could have been some times that I did, I don't know for sure. I do know, however, that it has never had anything to do with cats. The first time I had this happen to me was probably around 2012. The very first Minecraft world I ever created, which was March 2011, had multiple incidents of chunks randomly being reset. I made several mines, and after I stopped playing the world for a while and came back, one of the mines, a spiral mineshaft down to a small room at bedrock level, was completely gone. I'm not even sure it was a very different game version; the terrain wasn't different, it was a completely flawless reset. I tried accessing the mine from an old underground shaft, but the shaft dead-ended instead. I later found that another whole area I had built on was reset. I have occasionally checked on the world, and now it is almost completely unidentifiable as the original world. Almost everything has been reset and changed. I can't even find my first house anymore. Nevermind I found it! But there's still parts of the world that were reset.
Please do not mark unreleased versions as affected.
You don't have access to them yet.
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