Optimizing worlds would 'corrupt' the world.

Well, I did optimize a world with a huge chunk count. Apparently optimizing a world to the latest format of the game just to clear cached data would leave the world look 'corrupted', maybe the huge number of chunks in it? I have no idea why such a thing like this were to happen. Heck, even the items and the inventory itself is 'corrupted'. What kind of bug is this? I think my world that I worked for so long, is doomed.