I've never heard of a cylinder (on a saw not used for racing) burning through in area lacking plating..., especially below the ports. Additional flaking occurring, possibly (but not necessarily imminent, either). Bare aluminum cylinders with plated pistons were common not that many years ago. I may be all wet, but have never worried about small areas of missing plating.
I would not use acid to clean up any cylinder with questionable plating or aluminum exposure. It will eat any exposed aluminum and destroy an otherwise perfectly salvageable cylinder that may only have some incidental streaking or gouges along with the typical aluminum x-fer that can be easily removed by any number of simple methods. Traditional honing should be avoided as it is too aggressive. 220 grit paper would be a good start to see what you can remove easily just using a drill with a split mandrel for the paper. You may be surprised at how well it cleans up while also putting a much more positive (and economical!) spin on the matter.
