I have no idea how to replicate it, but it's happened multiple times. I'm playing in singleplayer.
I have no idea what's happening, but occasionally chunks will re-load back into the world, undoing all of the changes i've made to it. in the attached screenshot, there's one example. it took me about a half hour to convert all of that lava to obsidian and mine it all out, uncovering about 30 diamonds in the process. (fortune III pick has it's uses.)
I spend roughly 90% of my time in this mine down here, and possibly a little bit going in and out of the nether. I don't think that the nether is what's causing this, though, because a chunk went bad before I'd even found diamonds, and cows keep appearing in the exact same mysterious places (out of their pen).
I will admit, I do have MCEdit, but I can pretty much guarantee that program isn't causing this, because the glitches were happening before I even used it on this world.
it doesn't make the game unplayable at the moment, but I need to re-mine all of that obsidian. on the plus side though... yay for more diamonds.