No, if you were just worried about energy, you would be much less tired than by doing things manually. For example, moving a heavy object downhill would gain you energy, not lose it, and keeping a heavy object in the air would neither gain nor lose energy. it would only be lifting that is hard, and it would still be easier than lifting manually.
Edit: and according to Wikipedia, human muscles only have an efficiency of around 20%, so doing basically anything through magic would be 5x easier than doing it by hand.
if the part of your body losing the mass was actually completely random, the atoms would disappear roughly evenly across your body, so probably the main thing you have to be worried about is your DNA (and thus getting cancer).