Random Chunk Regeneration

The world I'm currently working on is a world I've had since at least before Beta 1.8. Unfortunately I've started to run into a problem. Occasionally, I'll launch the game and enter the world only to find that one or more chunks have regenerated. Because of the number of worldgen changes that have occurred since I started the world, the new randomly generated chunk is without fail a different biome and height from the one it replaced and the surrounding chunks. Oftentimes it wipes out areas that I have built up, but some of the areas are only lightly touched.

Now fortunately I have carbonite, so I can usually revert the affected files and launch the game again. The issue has never occurred identically twice in a row, even when loading from an identical set of files.