If you look in my goose egg thread there are links to a clorox pdf about sanitizing waterfowl eggs. I had 3 grow bacteria after I put them in my bator so it is a good thing to wash them off. I used fine steel wool to clean my goos eggs up.
The bloom on duck eggs is really thick and I try not to scratch it as it protects the eggs from bateria, can you believe that the really yucky eggs hatch under momma ducks without a problem. To clean them up, I get a wet paper towel and wrap them up in it for a couple of moments. Then just use it to lightly wipe it off, leaving the egg clean and the bloom intact. I try not to use anything abrasive on eggs.