First, use a brake cleaner and plenty of paper towels.

Then you can use an angle grinder with a flap type sanding wheel (I like Norton brand wheels) to scuff the surface a wee bit, then spray it again. You should be good to go.

I do not know what the specification is on how thin you can turn the flywheel. After a while, I would be concerned just as much about its balance.

I would treat it the same as the brake rotors. As long as you do not have hard spots, usually bluish or warping, there is no need to reface them. One has to be an aggressive or a neglecting driver to warp a flywheel or grind in the rivets into one.

Phil