Sandpaper
On something as large as a roof? Are you crazy?
I would try some kind of powered buffer ; or at least an attachment you can put on a normal drill.
Crazy is as crazy does. (I have no idea what that means, so don't ask) The whole point of copper as an exterior finish is the attractive patina it acquires - whether it's an ancient bronze state, the Statue of Liberty, a medieval cathedral or some neo-Victorian house. The patina protects the rest of the copper from further corrosion, and varies over time and across the surface. The sandpaper comment by Borek was just to club the point home for the original poster.
You carefully sand the copper to it's bare metal. Presumably, you apply a lacquer, to prevent further corrosion, this process must be done rapidly, because the copper will begin corroding again quickly. You'll have to reapply this lacquer periodically, because it will wear off. All to have the only roof in the world that still has a newly minted copper penny color. Meh, to each his own but ...
Copper is pretty expensive. You might be surprised how thin the flashing is. Too much sanding, and you're going to go through.