If the nickel does flake off it is evident when examining cases and I would not use them further. In general it should not be a problem if the cases are plated correctly, sometimes they are not plated properly and this can happen much like chrome will peel off a car bumper if the process of plating was incorrectly done. There is no reason to nickel plate brass cases except manufacturers know the appearance of nickel plated cases will appeal to some buyers because they think they look 'Kool', but is unnecessary and useless nor does it give cartridges special powers.
I've used nickel brass a few times when regular brass wasn't available and nickel cases were the only option at the time. Never had a problem and reloaded them over a dozen times without flaking or ruining my dies. This was 300WSM cases I picked up at the range, necked down, false shouldered and fire formed blowing the shoulder ahead to use in a 7WSM. If that didn't flake the nickel off not much else will. If nickel is flaking the plating process was faulty, if it does happen cease using them.