Le Fluffie should do it - remove .gpd, update gamerscore, etc. (rebuild package).
it should have been as long as you havn't logged into live since you got the achievement. open your profile (ex. E345678901233) in lefluffie, modio, or your program of choice. look in the contents for the .gpd associated with the emulator (ex. 4569871.gpd) and delete it. now save, rehash, resign and you should be good after that.
Gamerscore, total achievements earned, etc. would have to be updated as well. It doesn't do all that just by deleting the .gpd.