I do it all the time. I put a pair of 81 Husky wheels in and they came out a treat and were bolted pretty much staight into a bike.. If there's any white scale on the alloy the paint on the hubs will lift, but it won't affect the anodising. The longer you can leave them in the better, but at least a week, two if you can wait that long. I have a green wheelie bin full and put anything that can fit in it, holds 6 mx wheels. Do it, you'll be wrapt with the results.
Cheers,
K