Daring to go where only the ignorant will, I would ask of the metrology aficionados, is not a cylinder square a "self proving" thing, which works by having the ends turned concave, with only a relatively narrow rim to stand on the surface plate?
Provided the cylinder curved surfaces are in good condition, not having to be reliant on how straight are the ways of a lathe, then if turned between centers, facing and finally lapping the rim in Y-Axis theoretically forces a square when standing on it's end, even if the rim is theoretically not flat. So long as the end surface feature "rings" go all the way around, it will still stand square.
Of course, it is much nicer to have the rim ends as flat as possible, and a square as possible to the cylinder, but not essential. The region is narrow, and so long as spun between centers, the cylinder will stand up square, forced by the geometry of being constrained between two points when made.
Proving it with a dial indicator on a surface plate will reveal whether one has made a metrology version of the leaning tower of Pisa.
I get it that one is talking about serious actions on an expensive metrology item, but is not the risk of re-finishing the ends minimal?
Also - while talking of vinegar, would not abut 5 microns of nickel prevent this happening again? The next question is, why are such things not given plating protection in the first place?