My server has had this issue in the past. What I had to do was literally learn the anvil file format enough to know which region file the chunk is located in and delete that one. The secret to this, is to take the coordinates of the corrupted chunks, and do some math with them.
Basically you take the X coordinate of the chunk, divide by 16 to reduce the chunks down to single digits, then divide by 32 because there are 32 chunks in each MCR File. This spits out the first number used in the file's name. Do the same for the Z coordinate, and you get the second number. You then have to delete the file the numbers match up to, and the region will be regenerated. Only downside is if you do the math wrong, or you have lots of things in the immediate vicinity of that chunk, it's going to all get wiped because of the region files. And you must round to the nearest whole integer if you get a number that doesn't divide evenly.
You can view more documentation on the Minecraft Region File Format here: http://www.minecraft...ki/Chunk_format
EDIT: Also, you can get the bees back by using an Imprinter if I remember correctly.