After updating to the most recent version of Minecraft, all of my previous achievements were lost.
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It is an annoying thing that really needs to be fixed. Possibly online syncing like they've been talking about since they were added to the game?
I have also had achievements reset. As Levon stated, I also have not had achievement reset after updates. I would also like to note that I loaded a backup of my achievements into my folder and after 3 tries they were not accepted.
I looked into the issue and it seems to be related to the fact that there are no MD5 hashes for newer achievements and blocks in map.txt in the achievement folder of minecraft.jar. There is a "checksum" value in the stats .dat file, and if this is incorrect, Minecraft empties the file. The checksum is the MD5 hash of the values in the following format:
local<HASH>,value,<HASH>,value,<HASH>,value, ...
So if your only statistic is 10 worlds loaded (Worlds Loaded's id is 1002, and 1002's associated hash in map.txt is d517ae73160fd8576d7687ead1c1a973:
locald517ae73160fd8576d7687ead1c1a973,10,
The hash of that string is 4c9841b44dca5b5667d220471ab70817, and that is what is used as the checksum value.
map.txt in minecraft.jar is a list of MD5s and statistics ids. The string starts with "local", then includes the id-hash and value of each statistic/achievement. But there are no hashes for any achievement id over 5242895 (newer achievements go up to 5242903 or so), and no hashes for any block introduced after the achievement system was added, such as Melon blocks. Obviously Minecraft knows how to handle these missing hashes since statistics for these blocks/achievements were stored prior to 1.4, but it may have something to do with the statistics-wiping of 1.4.
I attached an example of a stats file that will be wiped upon loading Minecraft 1.4. Remember to change the filename from "Player" to your username to make Minecraft actually handle it.
You can edit the stats of your player found in your wolrd's folder. [minecraft|http://hopper.minecraft.net/help/finding-minecraft-data-folder]/saves/<worldname>/stats/<playername>.json
I believe this happens every time you update Minecraft, or manually upgrade with a snapshot. I agree that this is a bug though and should be looked into to see if there is a fix/workaround.