I\'ve repainted a few WotC prepainted Star Wars figures, including minor conversions. I haven\'t had any problems with paint flaking off or anything.
I dip them in an acetone bath and scrub them with an old toothbrush to get the old paint off. I wouldn\'t recommend leaving them in the acetone for too long as the figure starts to soften a little, but for 30 seconds or so it\'s okay. Try it with a common figure first just in case.
I prime white with a spray primer, and I don\'t have any problems. Obviously, I don\'t throw the figures into a cardboard box after repainting them, but treat them like any metal figure.