If within your Do loop you know the index of the value that you want to exclude (and suppose that index is k), then outside of your Do loop you could use
w = Flatten[Table[{y/100}, {y, 50}]]
e = Range[1, 50]
and within the Do loop (which I assume determines the index k in some fashion)
z = RandomChoice[Delete[w, k] -> Delete[e, k], 1]
which just removes that item from both w and e and makes the random selection.
